A substrate processing system has a housing that defines a process chamber. A substrate holder disposed within the process chamber supports a substrate during substrate processing. A gas-delivery system introduces a gas into the process chamber. A pressure-control system maintains a selected pressure within the process chamber. A high-density plasma generating system forms a plasma having a density greater than 1011 ions/cm3 within the process chamber. A radio-frequency bias system generates an electrical bias on the substrate at a frequency less than 5 MHz. A controller controls the gas-delivery system, the pressure-control system, the high-density plasma generating system, and the radio-frequency bias system.