A registration device, including a wand, a light guide passing through the wand, and a position sensor fixed to the wand. A light source outputs a modulated beam of light into a light guide proximal end, so that the light is emitted from a light guide distal end toward a surface in proximity to a wand distal tip. A detector receives, from the light guide proximal end, light reflected from the surface into the light guide distal end, and outputs a signal indicative of the reflected light intensity. A processor computes a distance from the distal tip of the wand to the surface by extracting a phase difference between the output beam and the reflected light from the signal, and computes a position of the surface in a sensor frame of reference responsively to the computed distance and the location of the distal tip found from the position sensor.