Using atomic force microscopy (AFM) and X-ray diffraction (XRD), we analyzed the growth of differently modified pentacenes (perfluoropentacene and pentacenetetrone) on graphite and demonstrate that both the resulting morphology and the crystalline structure of the films critically depend on the microroughness of the substrate. On well-ordered highly oriented pyrolytic graphite (HOPG) surfaces prepared by exfoliation, both molecular materials form exceptionally smooth films, which consist of large-area molecularly flat islands yielding an overall low roughness. Interestingly, in these films molecules adopt a recumbent orientation, while on defective substrates, created by brief ion sputtering, the molecules adopt an upright orientation and form nonconnected islands exhibiting a significantly increased film roughness. Our study not only underlines the possibility to prepare very smooth films on a weakly interacting substrate but also emphasizes the importance of a proper substrate preparation and the significance of precise knowledge of substrate-surface properties to control the resulting structure of organic films.