A wavelength scanning interferometer for measuring the surface and thickness of a transparent film has been studied. A halogen light source combined with an acousto-optic tuneable filter is used to generate a sequence of filtered light in a Linnik interferometer, which leads to a sequence of interferograms captured by a CCD camera. When a transparent thin film is measured, the reflection signals from both the top and bottom surfaces of the film will interfere with the reference signal. At the same time, the multiple reflection signals between the two film surfaces will also interfere with each other. Effective separation of the interference signals from each other is the key to achieving a successful measurement. By performing a frequency-domain analysis, these interference signals can be separated. An optimized Fourier transform method is used in the analysis. Measurements of the top and bottom surface finishes of the film, as well as the film thickness map, have been achieved. The film needs to be more than 3 μm in optical path length, and must transparent with no absorption of light. The film's refractive index needs to be known as a function of wavelength. In this paper, the theoretical analysis and simulation study of wavelength scanning interferometry for transparent film measurement is discussed. Experiments on thin film layers of Parylene N coated on a glass slide surface are studied and analyzed. Comparison study results with other contact and non-contact methods are also presented.