1. A non-transitory computer readable storage medium storing computer executable instructions which when executed on a computer perform a method comprising: creating a three-dimensional bone model of a subject bone of a patient; comparing at least a portion of the bone model to at least one three-dimensional reference anatomic model, wherein the at least one three-dimensional reference anatomic model is a negative space reference anatomic model representing the shape of a void in an anatomically normal bone corresponding to the subject bone of the patient, and the step of comparing at least a portion of the bone model to at least one three-dimensional reference anatomic model includes the step of mating the at least one reference anatomic model to the bone model; identifying at least one structural difference between the bone model and the at least one reference anatomic model; and specifying at least one desired subject bone structural change to produce a modified bone model responsive to the step of identifying the at least one structural difference between the bone model and the at least one reference anatomic model, the modified bone model incorporating the at least one desired subject bone structural change configured to bring the subject bone of the patient closer to a normal anatomic bone structure represented by the at least one reference anatomic model.