The invention relates to a method and system for its implementation for referencing or registering a body part in a camera-assisted, medical navigation system, comprising: manually manipulating a light beamer so as to scan a light beam produced thereby across a surface of the body part to sequentially reflect light off the surface of the body part at a plurality of locations; sequentially detecting the light reflected from the surface of the body part at the plurality of locations; determining three-dimensional spatial positions of the plurality of locations based on the detected light; and referencing or registering the body part to medical image data based on the three-dimensional spatial positions of the plurality of locations and surface data determined from the medical image data.