Radio frequency (RF) diode sputtering has been used for the growth of giant magnetoresistive (GMR) metal multilayers. Control of the atomic-scale structure of the surfaces and interfaces within these films is critical for GMR applications. A systematic series of experiments have been conducted to evaluate the dependence of the magnetotransport properties upon the growth conditions (i.e. background pressure, input power) for NiFeCo/CoFe/CuAgAu spin valves during RF diode sputter deposition. By using computational fluid dynamics, plasma, molecular dynamics, and various Monte Carlo techniques, a multiscale modeling approach has investigated the atomic assembly events during film growth. Energetic metal atoms and inert gas ion fluxes are shown to have very strong effects upon interfacial structures. The insights gained have led to novel deposition strategy propopositions for interface morphology control.