White-light interferometry has a good performance to measure opaque surface profile and step height; While a transparent film is measured, because two beam of lights came from transparent film surface and substrate interfere with the reference light, interference fringe appears twice at the same point and two coherence-peaks be found in the correlogram. The location algorithm of single coherence peak is computed near the maximal intensity and do not judge which interference fringe is come from film surface, so it is not sure to extract the film surface and to know the thickness of film. In this paper, the characteristic of correlogram came from transparent film is utilized to analyze the peak separation algorithms of envelope, and these algorithms are compared through results. Theoretical analysis and experiment result show that the surface and thickness of transparent film measured by white-light interference microscope have high precision when the two coherence peaks at film surface and film substrate are efficiently separated by separation algorithms.