Thin films of the organic molecule perylene-3,4,9,10-tetracarboxylic-dianhydride ("PTCDA") on graphite(0001) have been investigated from the mono-to the multilayer regime with low energy electron diffraction (LEED), X-ray-diffraction in Bragg-Brentano geometry, and high resolution scanning tunneling microscopy (STM). These different methods proved epitaxial growth in a coincident superstructure and yielded congruent results concerning details of the crystallographic structure of the epilayer. In addition it was possible to resolve submolecular structures in high resolution STM images; a comparison of the 10 resolved maxima of the tunneling current with the molecular structure leads us to question the conventional model description of tunneling.