A medical device for preparing a bone of a joint of a patient includes a numerically controlled instrument having a housing including a controller, a processor and a tool driver, a patient-specific reference guide removably couplable to the housing, and a cutting tool removably coupled to the tool driver. The patient-specific reference guide has a three-dimensional inner surface preoperatively configured to mirror and mate with a corresponding surface of a bone of a joint of a patient in only one position. The patient-specific reference guide is configured to automatically register the numerically controlled instrument to the patients bone portion intraoperatively. The cutting tool is movable along a patient-specific tool path determined during the preoperative plan for preparing a portion of the bone.
