Automated robotic system for handling surgical instruments

Systems and methods that process a plurality of surgical instruments for cleaning and/or packaging. A device identifies a robot-ready insert having a predetermined configuration for accepting at least one type of surgical instrument. The surgical instruments are identified and oriented according to type using an automated apparatus. Specialized tools are also provided for automatically opening and closing surgical instruments, flipping instruments and assisting in the processing and maintenance of surgical instruments. The automated apparatus then places each of the surgical instrument types in one or more predetermined areas of the insert, configured to accept a predetermined set of surgical instrument types.