A diverse array of self-organized nanoscale morphologies evolve during physical vapor deposition of phase-separating alloy films. However, our understanding of the different material and process parameters and how they influence the formation of these nanostructures is fairly limited. Here, we develop a phase-field model which is capable of predicting the entire spectrum of nanostructures as a function of processing conditions in vapor-deposited Cu-Mo films. We adopt a double well free energy formalism that has previously been used to simulate phase separation in immiscible fluids and di-block copolymers, quantitatively. We numerically investigate the influence of substrate interaction, deposition rates, phase volume fraction, and temperature, on the morphological self-assembly of nanostructures in vapor-deposited alloys. Based on our parametric study, we deduce morphology maps and explore the possibility of new nanoscale features by choosing different combinations of processing conditions. Computational mechanical tests of the simulated nanostructures are performed to extract structure-property relationships. Insights gained from our findings will help develop new pathways for morphology control in the manufacturing and design of immiscible alloy films.