Radio frequency (RF) diode sputtering deposition is a widely used process for depositing GMR thin films for multilayers, spin valves, spin-dependent tunneling (SDT) devices, etc. However, the thin films thus produced often show significant variation in GMR properties from wafer to wafer. A multiscale model based on the primary physical phenomena – gas flow, plasma discharge, sputtering and atom transport has been developed to explore the sputter deposition process. Simulations with this model were used to determine the process parameters to which the deposition characteristics have the maximum sensitivity. Experiments were performed to determine the relative importance of these parameters. Based on the results, a controller was designed to regulate the time-integrated target bias voltage. Implementation of the controller reduced wafer-to-wafer variation of GMR properties by over 50%. Additionally, application of control to SDT wafers also led to improvement and optimization of the process.