In this communication, we describe a fast thickness profile measurement method for a transparent film, thinner than the white-light coherence length of 3-4 mum that is deposited on pattern structures. A visible acousto-optic tunable filter is employed for real-time wavelength scanning and the three-dimensional volumetric thin-film thickness profile information is obtained using a simple peak detection method in the spectral domain. The key idea is to divide the measurement into two states using a beam blocking mechanism to separately obtain the two unknowns of thickness and surface profile. Such separate measurements are required to compensate for the phase change effect caused by the multi-reflected beams from the thin film. The final thin-film surface profile information is measured by obtaining the number of peaks and phase deviations from the two separately scanned spectral intensity values.