Molecular vacancies form in both of the crystallographic basis sites of thin pentacene crystals. Features in scanning tunneling microscopy images of these crystals correspond to the exposed terminal atoms of molecules. The (001) and (00 (1) over bar) surfaces of pentacene are distinguishable, which allows for the identification of the absolute orientation of crystals and for the unambiguous assignment of the position of molecules relative to each vacancy. For vacancies in each molecular basis site of the pentacene (001) surface, the image feature associated with one molecular nearest neighbor is displaced by significantly more than other molecules. (c) 2008 American Institute of Physics.