The intriguing photophysical properties of monolayer stacks of different transition-metal dichalcogenides (TMDs), revealing rich exciton physics including interfacial and moiré excitons, have recently prompted an extension of similar investigations to hybrid systems of TMDs and organic films, as the latter combine large photoabsorption cross sections with the ability to tailor energy levels by targeted synthesis. To go beyond single-molecule photoexcitations and exploit the excitonic signatures of organic solids, crystalline molecular films are required. Moreover, a defined registry on the substrate, ideally an epitaxy, is desirable to also achieve an excitonic coupling in momentum space. This poses a certain challenge as excitonic dipole moments of organic films are closely related to the molecular orientation and film structure, which critically depend on the support roughness. Using X-ray diffraction, optical polarization, and atomic force microscopy, we analyzed the structure of pentacene (PEN) multilayer films grown on WSe2(001) and WS2(001) and identified an epitaxial alignment. While (022)-oriented PEN films are formed on both substrates, their azimuthal orientations are quite different, showing an alignment of the molecular L-axis along the and directions. This intrinsic epitaxial PEN growth depends, however, sensitively on the substrates surface quality. While it occurs on exfoliated TMD single crystals and multilayer flakes, it is hardly found on exfoliated monolayers, which often exhibit bubbles and wrinkles. This enhances the surface roughness and results in (001)-oriented PEN films with upright molecular orientation but without any azimuthal alignment. However, monolayer flakes can be smoothed by AFM operated in contact mode or by transferring to ultrasmooth substrates such as hBN, which again yields epitaxial PEN films. As different PEN orientations result in different characteristic film morphologies (elongated mesa islands vs pyramidal dendrites), which can be easily distinguished by AFM or optical microscopy, this provides a simple means to judge the roughness of the used TMD surface.