A system and method for measuring defects, film thickness, contamination, particles and height of a thin film disk or a silicon wafer. The system includes a processor for determining height. In addition to measuring the height the system can measure film thickness and defects through the measurement of the phase shift of optical signals. An optical profilometer is described which can measure topography on thin film disks, optical substrates or silicon wafers and whose output is independent of the reflectivity of the substrate. This material independent optical profilometer uses a retro-reflector to achieve reflectivity independence and to increase the height sensitivity to 8 times the height of the surface. The reflectivity independent optical profilometer achieves perfect cancellation of the slope of the surface while measuring the topography of the substrate.