A pulsed plasma system with pulsed sample bias for etching semiconductor structures is described. In one embodiment, a portion of a sample is removed by applying a pulsed plasma process, wherein the pulsed plasma process comprises a plurality of duty cycles. A negative bias is applied to the sample during the ON state of each duty cycle, while a zero bias is applied to the sample during the OFF state of each duty cycle. In another embodiment, a first portion of a sample is removed by applying a continuous plasma process. The continuous plasma process is then terminated and a second portion of the sample is removed by applying a pulsed plasma process.