Herein investigation of the effects of substrate temperature on the structural and morphological features of both cobalt(II) phthalocyanine (CoPc) and cobalt(II) hexadecafluorophthalocyanine (CoPcF16) thin films is presented. For these purposes thin films of CoPc and CoPcF16 prepared by organic molecular beam deposition were investigated by means of optical absorption spectroscopy, X-ray diffraction, Raman spectroscopy, and atomic force microscopy. Concerning the degree of crystallinity, the morphology, the phase composition and the preferential molecular orientation of both CoPc and CoPcF16 thin films, we found out that the increase of substrate temperature during growth influences these properties of the above-mentioned thin film systems (CoPc vs. CoPcF16) in a different way. (C) 2010 Elsevier B.V. All rights reserved.