We have undertaken multi-lengthscale simulations to understand how the performance (as measured by the order) of organic thin films is affected by the choice of organic molecule, substrate surface, and deposition conditions. The bonding interactions of pentacene molecules and thiophenes on a variety of surfaces (Si, oxide, metals) has been investigated using a combination of tight-binding simulations, ab initio Gaussian™ 03 calculations, kinetic Monte Carlo and Molecular Dynamics approaches. Each approach provides a different, and often complementary, piece of the puzzle to help understand how small organic semiconducting molecules deposit and grow into thin films with differing final properties. For instance, a fairly comprehensive set of Gaussian-derived adsorption energies allows the determination of preferred binding configurations as observed in experimental STM images. These same energies can also be used as the input to a mesoscopic scale study of the layer-by-layer deposition of organic thin films in lattice-based Kinetic Monte Carlo simulations to provide a rich and varied set of morphological “maps” that depend on a delicate balance between molecule-molecule and molecule-substrate interactions.