An improved marker system, components and method for use with a medical navigation system, wherein the marker system includes interchangeable tracking marker holders and fastener bases for attaching the marker holders to instruments or body parts that are to be tracked during a medical procedure. A reference star (the marker holder and tracking marker(s)) and fastener base are removably attached to one another. This enables different reference stars to be interchangeably attached to a given fastener base, or vice versa, thereby to provide the best combination of reference star and fastener base for a given application. This preferably is accomplished by a standard interface between the fastener base and the holder for the tracking markers, e.g., reflective markers. In addition, surgical instruments may have integrally formed therein the standard interface, thereby eliminating the need for a fastener base.