The morphology and microstructure of metallic thin films synthesized by physical vapor deposition are known to be sensitive functions of the incident flux, its angular distribution and kinetic energy as well as the substrate temperature. Using an embedded atom method to represent the interatomic interactions, two-dimensional molecular dynamics simulations have been conducted to identify the role of these variables upon vacancy formation and surface morphology evolution during nickel deposition. The results reveal the existence of a critical incident angle above which mono-vacancies and vacancy clusters/voids are created by atomic shadowing. Increasing the substrate temperature and the adatom kinetic energy in the 0.1–2.0 eV range significantly reduces vacancy formation. Time lapse analyses have been used to identify the atomic mechanisms for this. They indicate that low defect concentration films can be synthesized at low temperatures by increasing the adatom kinetic energy to a few eV. A simple empirical model is proposed to relate the vacancy concentration to the controllable process conditions.