A surgical hardware and software monitoring system and method allows for surgical planning while the patient is available for surgery, for example while the patient is being prepared for surgery so that the system may model the surgical site. Tracker obtains image information, with controller configured to spatially relate image information with previously obtained scan data. Fiducial reference is configured for removably attaching to a location proximate a surgical site. The fiducial reference is observable by the tracker so that software of the controller determines three-dimensional location and orientation based on scan data and image data of the surgical site, spatially relating the image information to the scan data to determine the three-dimensional location and the orientation of the fiducial reference. In one embodiment, the model may be used to track contemplated surgical procedures and warn the physician regarding possible boundary violations that would indicate an inappropriate location in a surgical procedure. In another embodiment, the monitoring system may track the movement of instruments during the procedure and in reference to the model to enhance observation of the procedure. In a further embodiment the monitoring system can be used to model and track the changes in the surgical site itself.