A training system for training a trainee to perform a surgical procedure on an anatomical region. The system includes a physical model of the anatomical region, a physical training instrument, a tracking system configured to track the location and orientation of the physical training instrument relative to the physical model, a display device, and a computer system. The computer system receives from the tracking system information indicating the location and orientation of the physical training instrument and generates and displays an augmented physical model and the physical training instrument. The display is updated based as the trainee manipulates the physical training instrument. After the trainee has completed the surgical procedure, the computer calculates a score based on the performance of the trainee. The score is a measure of the accuracy of the surgical procedure performed by the trainee or the duration of the surgical procedure.