A system and method creates a patient-specific surgical plan for use during a surgical procedure. The plan may reference an instrument for registering a portion of a patient during the procedure. The plan may be based on a computer-generated model of a portion of the patient's anatomy. The plan may be provided to a surgeon who uses the registration instrument to register the portion of the patient's anatomy according to the plan. Spatial location data for a plurality of points on the instrument and/or on the patient's anatomy may be obtained, and a patient-based coordinate system may be established using the registration instrument, the captured spatial location data or combinations thereof. The coordinate system may be used to attach one or more prosthetic components to the patient at locations and/or orientations specified in the plan.
