Organic semiconductors combine flexible tailoring of their optoelectronic properties by synthetic means with strong light−matter coupling, which is advantageous for organic electronic device applications. Although spatially selective deposition has been demonstrated, lateral patterning of organic films with simultaneous control of molecular and crystalline orientation is lacking as traditional lithography is not applicable. Here, a new patterning approach based on surface-localized F-centers (halide vacancies) generated by electron irradiation of alkali halides is presented, which allows structural control of molecular adlayers. Combining optical and atomic force microscopy, X-ray diffraction, and density functional theory (DFT) calculations, it is shown that dinaphthothienothiophene (DNTT) molecules adopt an upright orientation on pristine KCl surfaces, while the F-centers stabilize a recumbent orientation, and that these orientations are maintained in thicker films. This specific nucleation results also in different crystallographic morphologies, namely, densely packed islands and jagged fibers, each epitaxially aligned on the KCl surface. Spatially selective surface irradiation can also be used to create patterns of F-centers and thus laterally patterned DNTT films, which can be further transferred to any (including elastomer) substrate due to the water solubility of the alkali halide growth templates.