1. A method of preparing for a surgical procedure, the method comprising the steps of: creating, using a computer, a three-dimensional bone model of a subject bone of a patient; comparing, using the computer, at least a portion of the bone model to at least one three-dimensional reference anatomic model, wherein the at least one reference anatomic model is a negative space reference anatomic model, and comparing at least a portion of the bone model to at least one three-dimensional reference anatomic model includes mating the at least one reference anatomic model to the bone model; identifying, using the computer, at least one structural difference between the bone model and the at least one reference anatomic model; and specifying, using the computer, at least one desired subject bone structural change to produce a modified bone model responsive to the step of identifying at least one structural difference between the bone model and the at least one reference anatomic model.