A minimally invasive robotic surgical system, comprising: a robotic surgical tool for performing a minimally invasive diagnostic or surgical procedure within a patient body, the robotic surgical tool having a distal end that is configured for insertion into and robotically manipulatable within the patient body, the distal end having three or more primitive features having known positions on the tool, wherein each primitive feature comprises a spherical reflective surface; wherein the three primitive features include a natural feature of the tool and an artificial feature of the tool; a light source configured for insertion into the patient body so as to be oriented to transmit illumination light toward the distal end of the robotic surgical tool when the distal end is within the patient body; a stereoscopic endoscope configured for insertion into the patient body so as to be adjacent the light source when the light source and the distal end of the tool are inserted in the patient body, so that the stereoscopic endoscope can capture stereo images of bright spots produced by the spherical reflective surfaces of the three or more primitive features as the illumination light is reflected from the primitive features toward the stereoscopic endoscope, the bright spots being substantially aligned with spherical centers of the spherical reflective surfaces; and a processor coupled to the stereoscopic endoscope and configured to determine a pose of the robotic surgical tool by processing the stereo images to locate the spherical centers of the natural feature of the tool, the artificial feature of the tool, and the third primitive feature of the tool by using the bright spots. a robotic surgical tool for performing a minimally invasive diagnostic or surgical procedure within a patient body, the robotic surgical tool having a distal end that is configured for insertion into and robotically manipulatable within the patient body, the distal end having three or more primitive features having known positions on the tool, wherein each primitive feature comprises a spherical reflective surface; wherein the three primitive features include a natural feature of the tool and an artificial feature of the tool; a light source configured for insertion into the patient body so as to be oriented to transmit illumination light toward the distal end of the robotic surgical tool when the distal end is within the patient body; a stereoscopic endoscope configured for insertion into the patient body so as to be adjacent the light source when the light source and the distal end of the tool are inserted in the patient body, so that the stereoscopic endoscope can capture stereo images of bright spots produced by the spherical reflective surfaces of the three or more primitive features as the illumination light is reflected from the primitive features toward the stereoscopic endoscope, the bright spots being substantially aligned with spherical centers of the spherical reflective surfaces; and a processor coupled to the stereoscopic endoscope and configured to determine a pose of the robotic surgical tool by processing the stereo images to locate the spherical centers of the natural feature of the tool, the artificial feature of the tool, and the third primitive feature of the tool by using the bright spots.