a method for using a medical navigation system to identify an instrument to be navigated is provided , wherein the instrument includes a reference array having a plurality of markers that form a rigid body , and a location of the markers with respect to each other is not previously known in the navigation system as a characteristic arrangement for a particular instrument . the method includes measuring a distance of each marker relative to the other markers ; identifying a spatial arrangement of the markers having the measured distance as an assignable marker array ; assigning the assignable marker array to the instrument ; and identifying the instrument based on the assigned marker array .