A method and apparatus for collecting and processing physical space data used while performing image-guided surgery is disclosed. Physical space data is collected by probing physical surface points of surgically exposed tissue. The physical space data provides three-dimensional (3-D) coordinates for each of the physical surface points. Based on the physical space data collected, point-based registrations used to indicate surgical position in both image space and physical space are determined. In one embodiment, the surface of surgically exposed tissue of a living patient is illuminated with laser light. Light reflected from the illuminated surface of the exposed tissue is received and analyzed. In another embodiment, one or more magnetic fields of known shape and size are established in the proximity of the exposed tissue. Data associated with the strength of the magnetic fields is acquired and analyzed.