Embodiments of the invention relate to a substrate etching method and apparatus. In one embodiment, a method for etching a substrate in a plasma etch reactor is provided that includes a) depositing a polymer on a substrate in an etch reactor, b) etching the substrate using a gas mixture including a fluorine-containing gas and oxygen in the etch reactor, c) etching a silicon-containing layer the substrate using a fluorine-containing gas without mixing oxygen in the etch reactor, and d) repeating a), b) and c) until an endpoint of a feature etched into the silicon-containing layer is reached.