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The increase of precision and minimal invasiveness is an important current issue in orthopedic surgery. The femur and the tibia must be shaped to fit an artificial joint for successful knee arthroplasty. The recent trend towards MIS (minimally invasive surgery) to decrease the length of the required incision has increased surgical difficulty, since the open access area is small. In this paper, registration and cutting error were analyzed with a robotic surgery system being developed first as an example, and a method of active compensation of robot deformation by gravity and cutting force was proposed and tried based on the error map with the expectation that the precision will increase.