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In order to realize high-performance organic thin-film transistors (TFT), two parameters of the organic semiconducting layer are desired: single crystallinity for high mobility and patterning for low off currents. High-quality single crystals can be fabricated using vapor techniques such as physical vapor transport (PVT), but they require high temperatures close to thermodynamic equilibrium, for example, 240 °C for pentacene. Such high temperatures are not ideal for TFT fabrication on plastic substrates and limit the use of PVT in flexible electronics applications. In this work arrays of pentacene single crystals were directly deposited at low temperature of 40 °C by vacuum thermal evaporation through microfabricated stencil masks (stencil lithography). By decreasing the stencil aperture size down to 1 μm × 1 μm, we were able to limit the nucleation area until only one grain per aperture is nucleated and grown. We studied systematically scaling effects for large singe crystal growth and discuss details of the growth morphology. We found for instance that the formed pentacene crystals are one monolayer thick and the crystal area is much larger than the aperture size. This can be explained by the diffusion of adsorbed molecules on the surface laterally under the shadow mask, where they are protected from other impinging molecules. The diffusion away from the impinging area under the aperture affects the nucleation density inside this area and was used to calculate the diffusion length to nucleation λN = 0.66 ± 0.11 μm of pentacene on SiO2 at 40 °C. Our diffusion-driven growth of organic single crystals by stencil lithography is a direct method to grow patterned arrays of single crystalline organic thin-film semiconductor layers.