Radio frequency (RF) diode sputtering is widely used for depositing Giant Magneto-Resistive (GMR) thin films for multilayers, spin valves,  and spin-dependent tunneling (SDT) devices used in data storage, computer memory, etc.  However, the thin films thus produced often show unacceptably high variation in GMR properties from wafer to wafer.  This paper describes a modeling and control effort that was undertaken for improving run-to-run repeatability.  A multiscale input-output model was developed for the primary physical phenomena in the deposition process − gas flow, plasma discharge, sputtering, and atom transport.  The model predicts the deposition rate, the energy distribution of sputtered atoms, and their sensitivity to deposition conditions such as power, working gas type, pressure, gas temperature, and electrode spacing.  Simulations with this model were used to determine the process parameters to which the wafer properties 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 led to improvement and optimization of the process.