The present invention involves a surgical monitoring system and method for modeling surgical procedures. A multi-element fiducial reference pattern observable by a tracker may be transferred directly to the skin proximate the surgical site, either through a stencil as a radio-opaque ink pattern or via transfer tape, or may be applied in prepared form on a surgical incise film. Alternatively the surgical incise film may be applied over the surgical site and the inked reference pattern applied to the film before surgery. A controller determines the three-dimensional location and orientation of the surgical site by comparing the position and orientation of the reference pattern in a prior scan with the position and orientation of the reference pattern in image information about the surgical site obtained from the tracker. The system may track the movement of instruments relative to the surgical site, or may be used to track changes in the surgical site itself.