A novel non‐destructive method for volumetric thickness profile measurement of a transparent film, thinner than the white light coherence length of 3∼4 &mgr;m, that is deposited on a patterned structure is described in this paper. A visible acousto‐optic tunable filter (AOTF) for wavelength scanning is employed and the 3 dimensional thin film thickness profile information is obtained through 2 phase functions &psgr;(k)and &fgr;(k)in the spectral domain. The first phase function &psgr;(k)compensates for the phase change effect caused by the multiple reflected beams from the thin film and the other is a total phase function &fgr;(k)for the interference between a reference mirror plane and the film deposited patterned structure. Compensation for the phase change effect was achieved by measuring the 3 dimensional film thickness information separately prior to surface profile measurement. Then the final thin film surface profile information was measured by using the total phase function obtained through spectral frequency domain signal processing. This total phase calculation algorithm is based on spectral carrier frequency concept. © 2003 American Institute of Physics