Methods for processing a substrate are provided herein. In some embodiments, a method of etching a dielectric layer includes generating a plasma by pulsing a first RF source signal having a first duty cycle; applying a second RF bias signal having a second duty cycle to the plasma; applying a third RF bias signal having a third duty cycle to the plasma, wherein the first, second, and third signals are synchronized; adjusting a phase variance between the first RF source signal and at least one of the second or third RF bias signals to control at least one of plasma ion density non-uniformity in the plasma or charge build-up on the dielectric layer; and etching the dielectric layer with the plasma.