A system for processing a substrate may include a first chamber operative to define a first plasma and a second chamber adjacent the first chamber, where the second chamber is electrically isolated from the first chamber, and configured to define a second plasma. The system may also include an extraction assembly disposed between the first chamber and second chamber to provide at least plasma isolation between the first plasma and the second plasma, a substrate assembly configured to support the substrate in the second chamber; and a biasing system configured to supply a plurality of first voltage pulses to direct first ions from the first plasma through the second chamber towards the substrate during one time period, and to supply a plurality of second voltage pulses to generate the second plasma and to attract second ions from the second plasma during another time period.