Efficient methodologies for synthesis of nanocrystals (NC) are a crucial component for creation of nanostructured electronic components. Physical vapor deposition (PVD) is one of the most flexible techniques to fabricate self-assembled arrangements of nanoclusters. Controllable fabrication of such assemblies can improve reliability of nanocapacitors, enhance performance of magnetic memories, and has many applications in opto-electronics devices, etc. However, size, shape and density of 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 greater detail. In this work, we present a kinetic Monte Carlo (KMC) model and report simulations that explicitly represent the PVD synthesis of nanocrystals on substrates. Here we study how varying the most important process parameters affects the morphologies of self-assembled metallic islands on substrates. We compare our results with experimentally observed surface morphologies generated by PVD and demonstrate that KMC models like this are an efficient tool for computer-aided design of PVD processes for synthesis of nanocrystals.