A method for preparing a bone of a joint of a patient includes mounting a patient-specific reference guide on a bone of a joint of a patient. A connecting portion of the reference guide is coupled to a miniaturized numerically controlled instrument having a housing including a controller, a processor and a 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 patient's bone portion intraoperatively. The cutting tool is guided by the controlled with signals from the processor along a patient-specific tool path determined during the preoperative plan for preparing a portion of the bone.