A system and method for generating a model of a patient specific cut guide instrument for harvesting a graft comprises a model of a graft defined by an implant interface surface, a bone interface surface, and a spatial geometry therebetween, the model being specific to a patient. A patient-specific instrument generator outputs the model of the patient specific cut guide instrument, the patient-specific instrument generator including a position determination module for orienting and positioning at least a first guide axis, and for positioning an abutment on a model of a donor bone as a function of the spatial geometry, and an instrument body generator module for generating a model of the patient specific cut guide instrument comprising a body supporting a cut guide to perform a depth cut in the donor bone positioned and oriented as a function of a contact of the body with the abutment on the donor bone, and of the model of the graft, a first guide channel for alignment with the first guide axis, and at least one anchor guide for securing the patient specific instrument cut guide on the donor bone as abutted with the abutment and aligned with the first guide axis, whereby the patient specific cut guide instrument is used for harvesting the graft for subsequent implanting without alterations to the spatial geometry of the graft.
