Cleaning Medical Instruments: Steps, Methods, and Best Practices

A medical instrument does not have to look dirty to be difficult to clean.

Blood, tissue, body fluids, and other material can get into hinges, grooves, joints, narrow channels, and other areas that are easy to overlook. Once that material dries, removing it becomes more difficult—and that can create problems for the steps that follow.

This is why cleaning medical instruments deserves more attention than simply rinsing an instrument or wiping away what you can see.

Cleaning is the stage where that contamination is physically removed. It normally involves water with a suitable detergent or enzymatic cleaner, along with manual friction or mechanical methods when appropriate. And importantly, cleaning comes before disinfection or sterilization; it does not mean the instrument is already sterile.

The tricky part is that there is no single cleaning method for every medical instrument. A basic metal instrument and a device with a hinge, narrow lumen, delicate surface, or multiple components may have very different reprocessing requirements. The manufacturer’s instructions for use (IFU) therefore matter throughout the process.

In this guide, we’ll break down what actually happens during medical instrument cleaning, why timing matters, where manual and ultrasonic cleaning fit in, how difficult-to-clean areas are handled, and what needs to happen before an instrument is returned to patient care.

The Medical Instrument Cleaning Process at a Glance

Stage	What is happening
Point-of-use treatment	Initial steps help prevent blood and other material from drying onto the instrument.
Cleaning	Organic and inorganic soil is physically removed.
Rinsing	Remaining soil and cleaning-agent residues are removed.
Drying	Moisture is removed before the next processing stage.
Inspection	The instrument is checked for cleanliness, damage, and integrity.
Disinfection or sterilization	The appropriate microbial-reduction process is performed based on the device and its intended use.

This sequence is a general framework, not a universal protocol. Reusable medical devices can differ substantially in their construction and cleaning requirements, so the manufacturer’s IFU and the healthcare facility’s validated procedures should determine the actual reprocessing method.

What Does Cleaning Medical Instruments Actually Remove?

When people hear the word cleaning, they often picture something simple: rinse the instrument, scrub away the visible material, and move on.

Medical instruments are a little different.

After use, an instrument may carry blood, tissue, body fluids, proteins, salts, and other organic or inorganic material. Some contamination may be obvious, while some can remain in hinges, grooves, joints, narrow channels, or other areas that are difficult to see and reach.

The purpose of cleaning is to physically remove that material from the device. CDC guidance emphasizes thorough cleaning before high-level disinfection or sterilization because residual soil can interfere with those subsequent processes.

Why Visible Cleanliness Is Not Enough

An instrument can look clean and still have residue left behind.

That matters because organic and inorganic material can interfere with subsequent disinfection or sterilization. Dried blood or tissue can be particularly difficult to remove and may interfere with the effectiveness of later processing.

So the goal is not simply to make an instrument look clean. The goal is to remove contamination well enough for the next stage of reprocessing to work as intended.

Why Timing Matters

Blood and other biological material are generally easier to remove before they dry onto an instrument.

For this reason, cleaning should begin as soon as practical after use. Point-of-use treatment helps prevent contamination from drying while the instrument is waiting for thorough cleaning later. It does not replace the full cleaning process.

Why Instrument Design Matters

Not every instrument presents the same cleaning challenge.

A simple metal instrument with an open surface may be relatively straightforward. An instrument with hinges, serrations, narrow channels, multiple components, or internal surfaces can be much harder to clean properly.

FDA guidance specifically identifies features such as long or narrow lumens, hinges, ridges, sleeves, and other soil-retaining areas as factors that can make reusable devices more difficult to reprocess.

That is why there is no sensible “one cleaning method fits every instrument” rule.

The Role of Cleaning Agents

Water alone may not remove every type of contamination. Medical-device cleaning commonly uses water with detergents or enzymatic cleaning products, combined with physical or mechanical action when appropriate.

The cleaning product also needs to be compatible with the instrument and the process being used. Using more chemical, a higher concentration, or a longer exposure simply because it seems stronger is not a substitute for following the device and product instructions.

An instrument being visibly clean does not mean it is sterile.

Cleaning removes contamination. Disinfection and sterilization are separate stages of reprocessing.

Cleaning vs. Disinfection vs. Sterilization: What Is the Difference?

These terms often appear together, but they do different jobs.

A useful way to think about them is:

Cleaning removes the material. Disinfection or sterilization deals with microorganisms that may remain.

What Is Cleaning?

Cleaning is the physical removal of soil and contamination from an instrument.

That soil may include blood, tissue, proteins, body fluids, and inorganic material such as salts. Depending on the device, cleaning can involve detergents or enzymatic cleaners together with friction, fluid flow, brushing, flushing, or mechanical equipment.

Cleaning is therefore not simply a weaker form of sterilization. It is a separate part of the reprocessing process.

What Is Disinfection?

Disinfection is intended to destroy many or most pathogenic microorganisms, depending on the level and method used.

It does not necessarily eliminate all forms of microbial life, particularly bacterial spores.

The required level depends on how the device is used. Devices that contact mucous membranes or non-intact skin have different processing requirements from devices that enter normally sterile tissue or the vascular system.

What Is Sterilization?

Sterilization is intended to eliminate all forms of microbial life to the level required by the validated sterilization process.

Critical medical devices that enter normally sterile tissue or the vascular system generally require sterilization before use.

But one point should never get lost:

Sterilization does not make inadequate cleaning acceptable.

Residual blood, tissue, or other debris can interfere with subsequent sterilization. Thorough cleaning has to come first.

A Simple Way to Remember the Difference

Process	Main job	What it does not replace
Cleaning	Removes soil and contamination	Disinfection or sterilization
Disinfection	Reduces or destroys microorganisms to the required level	Proper cleaning
Sterilization	Eliminates all forms of microbial life to the validated level	Proper cleaning

The exact combination of these stages depends on the device and its intended use. FDA describes reusable-device reprocessing as a multistep process in which devices are cleaned and then disinfected or sterilized according to their specific requirements.

How to Clean Medical Instruments: A Step-by-Step Process

There is no single cleaning routine that works for every medical instrument.

A simple open-surface instrument is very different from a device with a hinge, narrow channel, multiple components, or delicate materials. The manufacturer’s instructions for use should therefore be the starting point for a reusable device rather than a generic cleaning recipe.

1. Start at the Point of Use

The cleaning process begins before the instrument reaches the reprocessing area.

Blood, tissue, and other biological material should not be allowed to dry onto the instrument unnecessarily. Dried or baked-on soil is harder to remove and can make later processing more difficult.

Point-of-use measures are intended to keep contamination manageable until thorough cleaning can be performed. They do not replace proper cleaning later.

2. Prepare the Instrument

Before cleaning begins, prepare the instrument according to its IFU.

For some devices, that may mean opening hinged parts or separating removable components. More complex devices may require specific disassembly or flushing because soil can remain inside areas that are difficult to reach.

If the manufacturer specifies how a device should be disassembled, cleaned, or flushed, those instructions should not be replaced with guesswork. FDA guidance notes that some soil-retaining designs may require disassembly unless effective cleaning without disassembly has been validated.

3. Clean Manually or Mechanically

Once the instrument is prepared, cleaning may be performed manually, mechanically, or with a combination of methods, depending on the device.

CDC recognizes manual cleaning as well as mechanical methods such as ultrasonic cleaners and washer-disinfectors.

Manual Cleaning

Manual cleaning relies heavily on friction and fluid movement.

A suitable brush can loosen soil from accessible surfaces, while fluid flow can help remove debris from internal channels when the device allows it.

The brush and cleaning accessories need to be appropriate for the device. A brush that is too large may not reach a channel properly, while inappropriate tools or excessive force could damage the instrument.

Manual cleaning also requires appropriate precautions because used instruments may contain blood or other potentially infectious material.

Mechanical Cleaning

Mechanical cleaning can provide additional or more consistent mechanical action when the equipment and instrument are compatible.

Examples include:

• Ultrasonic cleaners
• Washer-disinfectors
• Other automated cleaning equipment

These methods are not interchangeable. The instrument must be compatible with the equipment, and the equipment should be operated according to its manufacturer’s instructions.

4. Reach the Difficult Areas

This is where medical instrument cleaning often becomes more complicated.

Hinges, joints, serrations, narrow lumens, internal channels, sleeves, and spaces between components can retain biological material. FDA specifically identifies these types of features as challenges in reusable-device reprocessing.

For instruments with internal channels, cleaning may require flushing, brushing, or another device-specific method. The correct connector, brush, flushing procedure, or other accessory should come from the applicable IFU.

A quick visual rinse is therefore not enough for many complex reusable instruments.

5. Rinse and Dry

After cleaning, the instrument should be adequately rinsed to remove loosened soil as well as remaining cleaning-agent residues.

CDC recommends adequate rinsing after cleaning because detergent or enzymatic-cleaner residues should not simply carry into the next processing stage.

The instrument should then be dried according to its applicable instructions. Internal channels and enclosed areas may need particular attention because moisture can remain where it is difficult to see.

6. Inspect Before the Next Stage

Cleaning does not end when the scrubbing or automated cycle finishes.

The instrument should be inspected for remaining visible soil as well as damage or defects that could affect further processing or function.

Pay particular attention to:

• Hinges and joints
• Serrated surfaces
• Lumens and channels
• Connections and removable components
• Cracks, corrosion, or other damage

If visible contamination remains, the instrument should not simply move forward because a cleaning cycle has already been completed. The result matters more than the fact that a cycle was run.

Once the device has been adequately cleaned, rinsed, dried, and inspected, it can move to the appropriate disinfection or sterilization stage required for that device.

Cleaning is not one action. It is a controlled process that prepares the instrument for everything that comes after it.

Ultrasonic Cleaning of Medical Instruments

Some instruments have areas that are difficult to reach with a brush. Hinges, small joints, serrations, and other hard-to-reach surfaces can retain soil even when the instrument looks reasonably clean.

This is where ultrasonic cleaning of medical instruments can be useful.

An ultrasonic cleaner uses high-frequency sound energy to create microscopic bubbles in a liquid. These bubbles form and collapse rapidly in a process called cavitation. The resulting mechanical action can help loosen soil from instrument surfaces and difficult-to-reach areas. CDC recognizes ultrasonic cleaners as one mechanical method for cleaning medical devices.

How Does Ultrasonic Cleaning Work?

Think of ultrasonic cleaning as adding mechanical action to the cleaning solution.

The instrument is placed in an appropriate solution, and ultrasonic energy travels through the liquid. Cavitation creates bubble activity around submerged surfaces, helping loosen material attached to the instrument.

That can be useful where ordinary wiping or brushing has limited access.

But ultrasonic cleaning is not sterilization. It is a cleaning method, and the instrument still needs whatever subsequent reprocessing is required for its intended use.

Which Instruments Can Benefit?

Ultrasonic cleaning may be useful for certain reusable instruments and accessories with difficult-to-clean surfaces.

However, not every instrument should automatically be placed in an ultrasonic cleaner. Device design, materials, construction, and the manufacturer’s instructions all matter.

What Should You Watch Out For?

The biggest mistake is treating an ultrasonic cleaner as a magic cleaning box.

The correct cleaning solution, loading arrangement, equipment settings, and device preparation all matter. Parameters such as temperature, time, and detergent concentration should not be guessed.

The cleaning bath itself can also become contaminated. CDC notes that used ultrasonic cleaning solutions can contain bacteria, so the bath should not be treated as inherently clean or antimicrobial.

The useful way to think about ultrasonic cleaning is simple:

It can improve mechanical removal of soil in suitable applications, but it does not remove the need for proper cleaning technique or validated reprocessing.

What Cleaning Solutions Are Used for Medical Instruments?

Medical instruments can carry blood, tissue, proteins, fats, salts, and other material that does not simply rinse away.

That is why cleaning commonly uses water together with a detergent or enzymatic cleaning product, along with physical or mechanical action.

The cleaning solution has to be appropriate for both the contamination and the instrument.

Enzymatic Cleaners

Enzymatic cleaners can help break down certain types of organic soil.

Depending on the formulation, enzymes such as proteases, lipases, and amylases can act on proteins, fats, and carbohydrates respectively.

But an enzymatic cleaner does not mean an instrument can simply be soaked and forgotten.

The solution still needs appropriate physical or mechanical action such as brushing, flushing, or another validated cleaning method. Enzymes can help with the soil; they do not replace the cleaning process itself.

Detergent Compatibility Matters

A cleaning product can be effective at removing soil and still be unsuitable for a particular instrument.

Reusable devices may contain stainless steel, plastics, polymers, coatings, or combinations of materials. An incompatible or incorrectly used cleaning chemical can contribute to corrosion, surface damage, or other problems.

CDC recommends using detergents or enzymatic cleaners compatible with the materials being cleaned and following the relevant product and equipment instructions.

What About pH?

Cleaning products can differ significantly in pH.

Neutral or near-neutral detergents are commonly used for medical devices. Some alkaline formulations may be appropriate for particular applications, but stronger alkalinity can also create compatibility or corrosion concerns for some materials.

So choosing a cleaning solution is not about finding the strongest chemical available.

It is about finding a product that is appropriate for the soil, compatible with the device, and used according to its instructions.

Why Rinsing Matters

Once contamination has been removed, the cleaning solution itself should not simply remain on the instrument.

Adequate rinsing removes remaining soil along with detergent or enzymatic-cleaner residues that could interfere with later processing.

The goal is not to use the strongest cleaner. The goal is to remove contamination without damaging the instrument or leaving behind another problem.

How Are Complex Medical Instruments Cleaned?

A flat instrument is relatively straightforward to clean. The challenge starts when an instrument has places where blood, tissue, or other soil can hide.

The FDA expects manufacturers such as hinges, narrow lumens, internal channels, sleeves, joints, and other enclosed areas as factors that can make reusable devices harder to reprocess.

Hinged Instruments

Hinges and joints can create small spaces where contamination remains hidden.

When the IFU requires it, hinged instruments should be opened or positioned so cleaning solution and mechanical action can reach those surfaces.

For automated cleaning, proper positioning can be just as important as the cleaning cycle itself.

Serrated or Rough Surfaces

Serrations, ridges, and uneven surfaces can give organic material more places to lodge.

These areas may need careful brushing or another device-specific cleaning method.

The goal is not simply to scrub harder. It is to use the right cleaning action in the places where contamination is most likely to remain.

Instruments With Lumens or Internal Channels

Lumens are among the more difficult parts of reusable medical devices because contamination may be inside the instrument rather than on an easily visible surface.

Cleaning may require flushing, brushing, or another method that allows cleaning fluid to reach the internal pathway. Some channels may not accommodate a brush at all, which is why the manufacturer’s instructions matter so much.

The correct connectors, brushes, flushing method, fluid volume, and sequence should come from the applicable reprocessing instructions.

Instruments With Multiple Components

Some devices need to be separated into components before cleaning so that surfaces hidden between them can be reached.

Whether a device should be disassembled—and how far it should be disassembled—depends on its design and validated instructions.

The same principle applies to delicate instruments:

Do not improvise a cleaning method that could damage the device.

Complex instruments require more than a stronger cleaner or a longer soak. They require a process that actually reaches the places where contamination can hide.

How Healthcare Facilities Verify Instrument Cleaning

Cleaning should not end with the assumption that an instrument is clean because it looks clean.

For straightforward instruments, visual inspection can identify obvious blood, tissue, or other visible residue. But some contamination can remain in areas that are difficult to see, especially inside lumens, around hinges, or between components.

Visual Inspection Comes First

After cleaning and drying, instruments should be inspected for remaining soil and for damage that could affect further processing or use.

If visible contamination remains, the instrument should not simply move to disinfection or sterilization.

CDC recommends inspecting equipment surfaces after cleaning and removing equipment that cannot be properly cleaned or processed.

Can Cleanliness Be Tested?

In professional reprocessing environments, cleaning verification can go beyond visual inspection.

Depending on the facility, device, and quality system, tests may be used to detect residual organic material or other indicators of inadequate cleaning.

The important distinction is that cleaning verification is not the same as sterilization monitoring. A sterilization indicator can provide information about a sterilization cycle, but it does not prove that blood or tissue was adequately removed beforehand.

What About Cleaning Validation?

Cleaning validation is broader than checking one instrument after one cycle.

The FDA expects manufacturers of reusable medical devices to validate recommended cleaning processes and demonstrate that their instructions can produce adequately cleaned devices. Validation can take into account challenging devices, clinically relevant soils, and difficult-to-access locations.

In practical terms, the hardest part of the instrument to clean deserves attention when the cleaning process is designed and evaluated.

If soil remains, the answer is not to hope the next stage will fix it.

You cannot reliably inspect your way out of a poor cleaning process, and you cannot sterilize away the need for proper cleaning.

Common Medical Instrument Cleaning Mistakes

Most cleaning problems do not come from a lack of effort. They happen when an important part of the process is skipped, rushed, or treated as interchangeable with another step.

1. Letting Blood or Tissue Dry

The longer organic material sits on an instrument, the harder it can become to remove.

Point-of-use treatment and cleaning as soon as practical after use help prevent blood and tissue from drying onto the device.

2. Cleaning Only What You Can See

A device can look clean on the outside while still containing residue inside a hinge, joint, serration, or narrow channel.

This is particularly important with complex reusable devices because their design can create areas where biological debris is difficult to reach.

3. Using the Same Method for Every Instrument

A simple metal instrument and a device with internal channels do not necessarily need the same cleaning approach.

Reusable devices require device-specific reprocessing instructions, which may specify particular brushes, disassembly steps, flushing methods, cleaning products, or equipment.

4. Assuming Sterilization Will Fix Poor Cleaning

This is one of the most important mistakes to avoid.

Residual blood, tissue, proteins, and other material can interfere with subsequent sterilization.

Sterilization is not a replacement for thorough cleaning.

Good cleaning is not about doing more of everything. It is about doing the right things, in the right order, for the instrument being processed.

Can Microbubbles or Nanobubbles Be Used to Clean Medical Instruments?

Microbubble and nanobubble technology is being studied as a possible way to improve cleaning, including research involving biomedical and medical-device applications.

The basic idea is that very small gas bubbles in liquid may interact with contaminants and surfaces in ways that help loosen or remove soil. Recent laboratory research has reported promising results for microbubble-based cleaning of contaminated surfaces and experimental surgical instruments .

But promising research is not the same thing as an established clinical reprocessing method.

Are Nanobubbles a Standard Cleaning Method?

Not at this point.

Micro- and nanobubble cleaning remains an emerging area of research rather than a universal replacement for manual, ultrasonic, or automated medical-device cleaning.

That distinction matters because reusable instruments need a cleaning process that has been appropriately evaluated for the specific device and followed according to its reprocessing instructions.

A laboratory result showing improved removal of contamination does not, by itself, establish that a bubble-based process can safely replace conventional reprocessing.

And claims that nanobubbles can automatically “sterilize” medical instruments should be treated cautiously.

A technology that helps remove contamination is not automatically a sterilization technology.

For now, microbubble and nanobubble technology is best viewed as an emerging research direction, not a standard replacement for established medical instrument cleaning methods.

Frequently Asked Questions About Cleaning Medical Instruments

What is the first step in cleaning medical instruments? +

Cleaning should begin as soon as practical after use. Point-of-use treatment can help prevent blood, tissue, and other material from drying onto the instrument, which makes later cleaning more difficult.

Can you sterilize a medical instrument without cleaning it first? +

No. Cleaning needs to come before sterilization. Residual organic or inorganic material can interfere with subsequent processing, so sterilization is not a substitute for thorough cleaning.

Is ultrasonic cleaning better than manual cleaning? +

Not automatically. Ultrasonic cleaning is one mechanical cleaning method and can be useful for certain hard-to-clean areas, but the appropriate method depends on the instrument and its reprocessing instructions.

Are enzymatic cleaners necessary for every medical instrument? +

No. Enzymatic cleaners are one option for removing organic soil. The appropriate cleaning product depends on the device, contamination, materials, and applicable instructions.

Do all reusable medical instruments follow the same cleaning process? +

No. Instrument design, materials, intended use, and manufacturer instructions can all affect the required cleaning and reprocessing procedure. Devices with hinges, lumens, or multiple components may require additional steps.

Bottom Line

Cleaning medical instruments is not simply about making an instrument look clean.

The real job is to remove blood, tissue, proteins, salts, and other contamination from the surfaces and hard-to-reach areas where soil can remain. That may require point-of-use treatment, manual cleaning, mechanical methods such as ultrasonic cleaning, appropriate detergents or enzymatic cleaners, rinsing, drying, and inspection.

What happens next depends on the instrument. Disinfection or sterilization may be required, and those processes should follow the device’s established reprocessing instructions.

The simplest way to remember the whole process is this:

Cleaning prepares the instrument. Disinfection or sterilization completes the reprocessing process.

And when an instrument is complicated, the safest approach is not to guess. Follow the manufacturer’s instructions and make sure the cleaning process actually reaches the places where contamination can hide.

Top Visited

• Ancestral Supplements Review (2026): Ingredients, Safety & Worth It?
• Rayze Coffee
• Methylene Blue Dosage, Benefits & Safety: 2026 Guide
• Ozempic vs Wegovy vs Zepbound: 2026 Clinical & Chemistry

References

1. Centers for Disease Control and Prevention (CDC). Cleaning. CDC — Cleaning
2. Centers for Disease Control and Prevention (CDC). Summary Recommendations: Cleaning of Patient-Care Devices. CDC — Summary Recommendations
3. U.S. Food and Drug Administration (FDA). How Are Reusable Medical Devices Reprocessed? FDA — Reusable Medical Devices Reprocessing
4. University of Illinois Urbana-Champaign, Carl R. Woese Institute for Genomic Biology. Scrubbing Bubbles: Microparticles Clean Wounds, Surgical Instruments With Tiny Bubbles. University of Illinois — Microbubble Research