A method of plasma processing includes performing a reactive species control phase, performing an ion/radical control phase, and performing a by-product control phase. The reactive species control phase includes pulsing source power to a processing chamber to generate ions and radicals in a plasma. The ion/radical control phase is performed after the reactive species control phase. The ion/radical control phase includes reducing the source power to the processing chamber and pulsing bias power to a substrate in the processing chamber. The by-product control phase is performed after the ion/radical control phase. The by-product control phase includes reducing the source power to the processing chamber relative to the reactive species control phase and reducing the bias power to the substrate relative to the ion/radical control phase.