Most dental offices have a designated area for instrument reprocessing that is separate from the dental treatment room. This is ideal, since cleaning, sterilizing and storing instruments in the same room where the delivery of patient care is provided increases the risk of cross-contamination.

Some instruments and materials are single-use only. Single-use items should be segregated in the operatory, and those that are sharp or otherwise pose a risk of injury must be discarded into a sharps container. Items without risk, such as a saliva ejector, can be thrown into the trash. Finally, the tray or cassette of reusable instruments is taken to the cleaning and sterilization area for processing The Centres for Disease Control and Prevention (CDC) states that, "Contaminated instruments should be handled carefully to prevent exposure to sharp instruments that can cause percutaneous injury. Instruments should be placed in an appropriate container at the point of use to prevent percutaneous injuries during transport to the instrument processing area." In addition, the Occupational Safety and Health Administration (OSHA) says, "The person handling the instruments through removal, cleaning, packaging and sterilization needs to use heavy-duty gloves to help prevent injury with sharp contaminated instruments." Although heavy-duty gloves (utility gloves) may feel more awkward than examination gloves, they provide extra protection while handling instruments during the cleaning, rinsing, drying, packaging and sorting procedures that take place during instrument reprocessing. Additionally, nitrile utility gloves are available in a variety of sizes, allowing a more secure fit.