We developed a unique robotic manipulation system that accurately singulates surgical instruments in a cluttered environment. A novel single-view computer vision algorithm identifies the next instrument to grip from a cluttered pile and a compliant electromagnetic gripper picks up the identified instrument. System is validated through extensive experiments. This research was motivated by the challenges of perioperative process in hospitals today. Current process of instrument counting, sorting, and sterilization is highly labor intensive. Improperly sterilized instruments have resulted in many cases of infections. To address these challenges, an integrated robotic system for sorting instruments in a cluttered tray is designed and implemented. A digital camera is used to capture an image of a cluttered tray. A novel single-view vision algorithm is used to detect the instruments and determine the top instrument. Position and orientation of the top instrument is transferred to a robot. A compliant electromagnetic gripper is developed to complete the gripping. Experiments have demonstrated high success rate of both instrument recognition and manipulation. In the future, error handling needs to be further reinforced under various exceptions for better robustness.