A method for making an insert for a bone structure located within a surgical site comprises operating on the bone structure with a materials removing tool to remove materials from the bone structure tracking in three dimensions the location and orientation of the bone structure tracking in three dimensions the location and orientation of the working tip of the materials removing tool creating a software model of the materials volume removed from the bone structure and making the insert based on model data within the software model. An associated system comprises a controller and a tracker for tracking a 3-D tracking marker rigidly attached to the bone structure and a 3-D tracking marker rigidly attached to the materials removing tool. A manufacturing device is used to manufacture the insert based on the model data from the controller.
