Thin films of hexadecafluorophthalocyanine (F16CuPc) were grown by organic molecular beam deposition (OMBD) under ultra high vacuum (UHV) conditions on oxidized Si(001) substrates. The film thicknesses ranged from 120 to 450 Å and the substrate temperature was varied from −150 to 300 °C. X-ray diffraction and atomic force microscopy (AFM) were used to characterize the structure and morphology of the layers. Spectroscopic ellipsometry was employed to determine the dielectric properties and to locate characteristic transitions between 1.4 and 3.7 eV. The correlation of the electronic properties with the molecular packing in the films is discussed. The results are compared to the case of F16CuPc films grown on stepped sapphire surfaces, which differ in their lateral ordering behavior.