We report kinetic Monte-Karlo (KMC) simulation of self-assembled synthesis of nanocrystals by physical vapor deposition (PVD), which is one of the most flexible, efficient, and clean techniques to fabricate nanopatterns. In particular, self-assembled arrays of nanocrystals can be synthesized by PVD. However size, shape and density of self-assembled nanocrystals are highly sensitive to the process conditions such as duration of deposition, temperature, substrate material, etc. To efficiently synthesize nanocrystalline arrays by PVD, the process control factors should be understood in detail. KMC simulations of film deposition are an important tool for understanding the mechanisms of film deposition. In this paper, we report a KMC modeling that explicitly represents PVD synthesis of self-assembled nanocrystals. We study how varying critical process parameters such as deposition rate, duration, temperature, and substrate type affect the lateral 2D morphologies of self-assembled metallic islands on substrates, and compare our results with experimentally observed surface morphologies generated by PVD. Our simulations align well with experimental results reported in the literature.