The structure and morphology of sexithiophene thin films vacuum-deposited on friction-transferred polytetrafluoroethylene (PTFE) substrates was investigated by optical and electron microscopy and electron diffraction. Highly birefringent 6T films are formed at high or low deposition rates. Electron diffraction indicates the presence of three different crystal populations differing by the orientation of the 6T molecular axis and/or the molecular plane. First, the strongest substrate/deposit interactions are based on epitaxy and lead to a well-defined, symmetric molecular arrangement (Type I) with the 6T molecular and the PTFE chain axes parallel and the 6T molecular planes tilted at +/-33 degrees to the substrate. Second, more "defective" orientations result from interactions with the bare glass surface (Type II) and with the PTFE film edges or ridges (Type III), respectively. As shown in a parallel study using spectroscopic techniques, these defective orientations have a definite impact on the overall optical properties of the sexithiophene thin films.