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Multilayer hybrid thin films consisting of alternating layers of organic and inorganic materials were fabricated with powder of copper-phthalocyanine (CuPc) and zinc selenide (ZnSe) by electron beam evaporator. The structural and optical characterization of multilayer hybrid thin film were carried out by using X-ray diffraction (XRD), atomic force microscope (AFM) and UV-Vis absorption spectroscopy. XRD patterns show two peaks of the orientation of (200) plane monoclinic structure in CuPc material and (111) plane cubic structure in ZnSe material where pair numbers of multilayer hybrid thin film higher than two pairs. With the variation in the number of pairs of CuPc/ZnSe, AFM images present almost similar morphology but the optical absorption spectra are significantly changed. Such spectral changes can be interpreted by the effect of the aggregate size and the characteristic of the multilayer hybrid structure.