System for registering a coordinate system associated with a pre-acquired model of an object with a reference coordinate system. The system includes a portable unit which includes a display, a tracking system for tracking the portable unit and a processor. The processor is coupled with the portable unit and with the tracking system. The processor determines the position and orientation of the portable unit. The processor further determines the position of at least one marker located on the object according to at least one of, a tracked pointer and respective position related information. The processor further displays registration related information on the display. At least one of the registration related information and the display location of the registration related information are related to the position and orientation of the portable unit. The position of the at least one marker, in the coordinate system associated with the pre-acquired model, is predetermined.