Combining 2D materials with functional molecular films enables the fabrication of van der Waals bound organic/inorganic hybrids that are of interest for future device architectures. Recently, the 2D dielectric hexagonal boron nitride (hBN) has received particular attention since exfoliation allows the preparation of crystalline layers which have been utilized as ultrathin dielectrics in electronic devices. Here, we have studied the formation and structure of molecular films of the prototypical organic semiconductors pentacene (PEN) and perfluoropentacene (PFP) on hBN. Special attention was paid to the influence of substrate surface defects on the film formation by comparing molecular films that were grown on hBN substrates of various quality, including single crystals (representing the most ideal surface), briefly ion bombarded substrates, and exfoliated flakes. While X-ray diffraction (XRD) yields precise information about the crystalline structure of films grown on (large) single crystals, it is hardly applicable to analyze the films formed on exfoliated flakes because of their small size. Here, we demonstrate that in the case of flakes detailed structural analyses of the molecular films are possible by combining atomic force microscopy (AFM) with microspot UV/vis spectroscopy and optical polarization microscopy. On well-ordered hBN single crystal surfaces both acenes form very smooth and epitaxial crystalline films where molecules adopt a recumbent orientation (even in 100 nm thick films). By contrast, both materials adopt an upright molecular orientation and different polymorphs on defective hBN surfaces and reveal distinctly different film morphologies. On exfoliated flakes, PFP shows a film structure similar to that on the hBN single crystals, while PEN films exhibit a structure as on defective hBN substrates. In addition, a pronounced decoration of defect steps, which are probably created by the exfoliation process, was observed for PEN leading to the formation of tall and extended fibers where molecules adopt a recumbent orientation. The present study reveals different robustness in film growth on exfoliated hBN flakes for various molecules, which has to be considered in their device integration, especially with regard to their optoelectronic properties such as light absorption or charge transport, which depend critically on the molecular orientation and crystalline order.