Systems and methods are provided for generating patient specific instruments for use as surgical guides. A region of interest within a body of a patient is scanned to provide a three-dimensional model of the region of interest. A first user is allowed to position a model of a selected implant with the three-dimensional model of the region of interest via a graphical user interface. A patient specific instrument model is generated from a generic patient specific instrument model according to the position of the model of the selected implant within the three-dimensional model of the region of interest and the position of at least one extension of the model that is not visible to the first user. A patient specific instrument is fabricated according to the patient specific instrument model.
