A combined microwave/RF reactive ion etching reactor was used to investigate low‐temperature anisotropic etching of silicon and radiation damage caused by ion bombardment during plasma treatment. This configuration gives a high etch rate and high etching anisotropy. Reactive ion etching of water‐cooled or liquid nitrogen‐cooled silicon substrates were carried out to study the effect of substrate temperature on the extent of surface contamination and radiation damage. Capacitance‐voltage and deep level transient spectroscopy techniques were used to correlate the reactive ion etching conditions with radiation‐induced damage. From these studies, we have shown that with appropriate RF biasing, anisotropic reactive ion etching without causing degradation of the silicon surface can be achieved.