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The primary purpose of cleaning. Surgical instruments and scopes is to remove all inorganic and organic bioburden material from the internal and external surfaces of flexible endoscopes. The secondary purpose of cleaning. The optimal cleaning protocol will break down bioburden and clean the surface. Is the Prerequisite for Sterilization. All disinfection processes, whether done manually or done automatically in a washer-decontaminator- disinfector, can only be effective if prior cleaning is adequate.