The orientation of semiconducting organic molecules, like in copper phthalocyanine (CuPc) thin films, is of importance for the electrical properties of organic/inorganic hybrid devices. Amorphous silicon films (a-Si), deposited onto crystalline Si-wafers by DC-pulsed magnetron sputtering, were utilised as substrates for the investigation. Crystalline silicon (111), with and without native oxide, was used as reference. Thin films of CuPc were fabricated using Organic Molecular Beam Deposition (OMBD) under high vacuum conditions (3 × 10 −7 mbar). For one group of the substrates the native SiO2 layer was removed by hydrofluoric acid, and the surface was Hydrogen passivated. The average molecular tilting angle of CuPc molecules on both substrates was calculated from the anisotropic absorption coefficients as determined by ex situ Variable Angle Spectroscopic Ellipsometry (VASE). Significant differences in the molecular orientation depending on the substrate and its preparation are observed. For H-passivated silicon substrates it is found that the tilting angle changes from (66 ± 5)• to (83 ± 9)• when going from crystalline to amorphous substrates. Furthermore, CuPc molecules grew on silicon with native oxide in a "standing up" configuration at an angle of 90• relative to the substrate. Isotropic layers of CuPc were produced at substrate temperatures of around −155• C.