The optical and electronic properties of organic semiconductor thin films are intimately coupled to their morphology at the atomic level. Atomic level morphology cannot be probed experimentally. However, molecular simulations can provide a means to examine the morphologies of thin films with unrivalled spatial resolution. By directly mimicking the process by which organic semiconductor thin films are produced experimentally using either solution or vacuum processing, we have generated realistic morphologies for both organic light-emitting diodes (OLEDs) and organic photovoltaics (OPVs). These morphologies have enabled us to explore factors related to efficiency including molecular alignment, aggregation, formation of percolation networks, and the presence of trapped solvent. The morphologies are highly predictive. For example, we showed that the higher outcoupling of OLEDs containing Ir(ppy)2(acac) as opposed to Ir(ppy)3 results from kinetic-trapping during deposition; that a TAPC:C60 bulk heterojunction with 5 wt % TAPC contains extensive hole percolation pathways; and how solution deposition affects the alignment of Ir(ppy)2(acac). These and other examples demonstrate how simulations can be used to understand the connection between morphology and device performance, which is key to the further development of organic semiconductor devices.