Lithography methods are commonly used to create structures in inorganic semiconductors like silicon but have not been widely applied to organic crystals. In this work, electron beam lithography (EBL) is used to pattern structures into single organic photomechanical crystals composed of 1,2-bis(2-methyl-5-phenyl-3-thienyl)perfluorocyclopentene. The electron beam creates amorphous regions of decomposed molecules, while the reactivity of the unexposed crystal regions is preserved under a removable Au coating. Exposure of the patterned crystal to 365 nm light causes ridges of amorphous material to increase in height by 30-70%. This height increase can be reversed by visible light exposure and undergo multiple cycles. The reversible surface morphology changes are strong enough to rupture a sheet of graphene placed on top of the patterned crystal. Surprisingly, the change in dimensions of the EBL features is an order of magnitude larger than the changes in overall crystal dimensions as deduced from X-ray diffraction experiments and microscopy observations. A dynamic extrusion model is presented to explain how nanoscale features imprinted into single crystals can amplify molecular-level photomechanical changes. This work demonstrates the capability of EBL methods to produce sub-micron structural features on single photomechanical crystals, providing a new route to monolithic light-powered actuator devices.