Abstract: A method and apparatus is claimed for measuring the distance between a slider and a transparent disk with sub-nanometer resolution. The flying height is measured by applying ellipsometry. The measurement is done by: providing a sampling light beam with adjustable initial polarization state by phase modulation, and with variable incident angles relative to the air film and reflecting the sampling light off of the specimen at a detection site forming a reflected light beam that is then reflected at the detection site again and then guided to both detectors for detecting the intensity and phase change of the light beam to determine the gap's thickness as well as passing some light to a microscope used for observation of the detecting site on the specimen.