A detailed scanning probe microscopy of microstructure and properties for first few crystalline molecular layers of organic semiconductor pentacene vapor deposited onto amorphous SiO2 substrates has been demonstrated. The micro structure of pentacene films is particularly important, as pentacene is a benchmark semiconductor for organic field effect transistors (OFET). A statistical analysis of the orientation between the second and first layer from TSM images reveals a well defined and preferred orientation. All scanning probe images and analysis are based on freshly grown pentacene films. The domains of epitaxial order lower friction and more positive surface potential than the non-epitaxial domains. Thus, a clear correlation is indicated between epitaxial order and electrical properties of polycrystalline films.