A method, apparatus and system for controlling the processing of a substrate within a process chamber are described herein. In some embodiments, a method of controlling a substrate process within a process chamber includes determining a position of a moveable magnetron in the process chamber relative to a reference location on a surface of the substrate and modulating a power parameter of at least one power supply affecting substrate processing based on the determined position of the magnetron to control, for example, at least one of a deposition rate or an etching rate of the substrate processing. In one embodiment, the modulated power parameter is a power set point of at least one of a direct current (DC) source power, a radio frequency (RF) bias power, a DC shield bias voltage, or an electromagnetic coil current of the at least one power supply.