We report on the evolution of phase-separated morphologies in co-sputtered Cu-Mo films as a result of varying substrate temperature and deposition rate during deposition. A transition from vertically-oriented concentration modulations to laterally-oriented modulations followed by randomly-oriented modulations was observed in the Cu-Mo films because of changing substrate temperature at constant deposition rate. A refinement of the Cu-Mo domains was observed at increasing deposition rate at a constant substrate temperature. A coarsening of phaseseparated domains was also observed with increasing substrate temperature. The phase separation kinetics that controlled film morphology were limited by the surface interdiffusion of each species as the film grew in thickness. Control over the surface interdiffusion length was achieved by altering the deposition temperature and material flux.