Embodiments for processing a substrate in a pulsed plasma chamber are provided. A processing apparatus with two chambers, separated by a plate fluidly connecting the chambers, includes a continuous wave (CW) controller, a pulse controller, and a system controller. The CW controller sets the voltage and the frequency for a first radio frequency (RF) power source coupled to a top electrode. The pulse controller is operable to set voltage, frequency, ON-period duration, and OFF-period duration for a pulsed RF signal generated by a second RF power source coupled to the bottom electrode. The system controller is operable to set parameters to regulate the flow of species between the chambers to assist in the negative-ion etching, to neutralize excessive positive charge on the wafer surface during afterglow in the OFF period, and to assist in the re-striking of the bottom plasma during the ON period.