The electronic absorption and surface morphology evolution of two types of molecular double layer thin films, copper phthalocyanine (CuPc) layer deposited on chloro[subphthalocyaninato]boron(III) (SubPc) layer, denoted as SubPc/CuPc, and vice versa, with various thicknesses were investigated using ultraviolet (UV)-visible spectroscopy and atomic force microscopy (AFM). Both types of double layer structures showed similar broadened absorption patterns in the UV-visible region that were consistent with the fitted spectra following simple linear combination of the single layer absorption spectra of the two materials. In contrast, the surface morphology of double layer structures was dependent on the order of deposition. For the CuPc/SubPc structures, surface morphology was characterized by elongated grains, which are characteristic of SubPc thin films, indicating that the morphological influence of the underlying CuPc layer on the subsequent SubPc layer was not large. For the SubPc/CuPc structures, however, the underlying SubPc layer acted as a morphological template for the subsequently deposited CuPc layer. It was also observed that the grain size of the CuPc layer varied according to the thickness of the underlying SubPc layer.