The recent emergence of molecular ultrathin films as candidates for functional electronic materials and photo catalyst has prompted numerous investigations on their crystalline structure and thin film formation. This article describes the role of the effect of the nature of substrate and substrate temperatures in molecular organization of copper (II) phthalocyanine (CuPc) on gold coated quartz substrates using conventional vapor deposition at high vacuum (similar to 10(-6) Torr). Surprisingly, the 100 nm thick CuPc films on the quartz substrates are as highly ordered as on the polycrystalline gold-coated quartz substrates. Importantly, the molecular orientation in the two cases is radically different. Field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) observations of the ordered crystalline films indicated that domains are grown from the bottom to the top of the film and are densely packed with little grain boundary. X-ray diffraction (XRD) pattern shows a sharp intense peak at high substrate temperature due to the beta-phase of CuPc. The crystal structure was dependent on the substrate temperature. UV-vis absorption spectra of the ordered solid films were recorded, showing unique dependences on the molecular alignments depending on the substrate and film deposition temperature. The curving of nanoribbons upon exposure to an electron beam was noticed from the changes in FESEM images. The fractal dimension of the assembly of nanostructures, in the films deposited at different temperatures on various substrates, has been estimated from FESEM images. The effects of substrates and substrate temperature on the surface morphology, optical properties, and fractal dimension have been discussed.