A method of patterning a gate stack on a substrate is described. The method includes preparing a gate stack on a substrate, wherein the gate stack includes a high-k layer and a gate layer formed on the high-k layer. The method further includes transferring a pattern formed in the gate layer to the high-k layer using a pulsed bias plasma etching process, and selecting a process condition for the pulsed bias plasma etching process to achieve a silicon recess formed in the substrate having a depth less than 2 nanometer (nm).