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.
