Linear least square fitting (LLS) analysis was applied to Auger depth profile data to verify the chemical information which was extracted by target factor analysis (TFA) from a Si(2.5 nm)/Mo(5 nm) thin multilayer sample. The chemical state assignment was confirmed by measurement with external standard samples and each spectrum was used as the basis spectra for LLS. The profiles from the Si LMM and Mo MNN peaks constructed by LLS showed the clear existence of silicide layers with different thicknesses less than 1 nm at each interface, which was confirmed by TFA and transmission electron microscopy cross section. The usefulness and problems of combining LLS with TFA for characterization of this kind of complicated multilayer sample are discussed.