A real-time Positioning system monitors and displays a real-time position and orientation (pose) of a Surgical device (25) relative to reference device (27) and internal structures of a subject during a medical procedure. Tracking targets (28) are affixed to a surgical device (25) and a reference device (27). The reference device is fixed to a target site of a subject. The tracked targets are interactively monitored by a tracking device (13) and their raw positions are converted (15) to a position and orientation (pose) of the surgical device and the reference device. A medical imaging device (11) acquires images of internal structures of the subject which is converted into computer models by a modeling engine (17).; The models of internal structures are correctly registered with models of the surgical instrument and the reference device into a single interactive representation assisting a surgeon in a medical procedure. A trajectory planner (23) may be employed to select a best path through a subject based upon user defined criteria, such as greatest overall density, least density, furthest from nerves, blood vessels, intersecting.the most diseased tissue, etc.