A system 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.
