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The SUPREX thin film refinement of x-ray diffraction ͑XRD͒ was used to quantitatively analyze the structure of thermally evaporated iron phthalocyanine ͑FePc͒ organic thin films as a function of growth temperature and postdeposition in situ annealing time. A bilayer model was necessary to refine the FePc XRD data. Results using this model provide clear evidence that the first molecular layer of FePc contacting the sapphire substrate differs from the subsequent uniformly spaced molecular layers, indicating a Stranski-Krastanov growth mode. The ␣-to-␤ structural phase transformation of FePc was observed as a function of substrate temperature. No significant effect of postdeposition in situ annealing time was observed. Atomic force microscopy ͑AFM͒ measurements reveal a temperature-dependent morphology as the FePc changes from grains, to extended films, and finally shows crystallite formation for increasing deposition temperature. Structural characteristics obtained by SUPREX refinement and AFM quantitatively agree for surface roughness and average molecular layer spacing.