An ambiguity-free optical tracking system (100) includes a position sensor unit (104), a control box (106), a computer (110) and software. The position sensor unit includes two cameras (121 and 122) that track a plurality of individual infra-red reflecting markers (160) affixed on a patient's skin. Coordinates of the cameras in a coordinate system of the cameras are determined as part of a system calibration process by intentionally creating ambiguous markers with two true markers. Using this information, an ambiguity elimination algorithm automatically identifies and eliminates ambiguous markers. A recursive backtracking algorithm builds a one-to-one correspondence between reference markers and markers optically observed during treatment. By utilizing a concept of null markers, the backtracking algorithm deals with missing, misplaced and occluded markers.