A robot-based system for processing racks used for transportation of articles in connection with an inactivation procedure, such as sterilization, disinfection, and decontamination. Robots are used to move full and empty racks between a plurality of a locations within soiled and clean areas of a workspace, including, but not limited to, a loading station where soiled medical instruments are loaded on the racks, washer/disinfectors for processing the medical instruments, and an unloading station where clean medical instruments are unloaded from the racks for sorting into trays.
