Control of film morphology is widely recognized as one of the limiting factors in the development of conjugated polymers for photonic and electronic applications. Surface polymerization by ion-assisted deposition (SPIAD) is shown to drive film morphology. A wide variety of structures form in the SPIAD polythiophene films, including islands, lamellar structures, nanoscale crystallites, and fractal-like growth patterns. Density functional theorymolecular dynamic simulations are utilized to illustrate the manner in the incident ions affect polymerization, bond dissociation, and other chemical events in SPIAD. These ion-assisted events mediate thermal processes such as neutral deposition, sublimation, diffusion, and dewetting. However, these thermal processes are on longer timescales that cannot be directly studied by the computational techniques reported here.