An apparatus and methods for selectively etching a particular layer are disclosed. The apparatus and methods are directed towards maintaining the etch rate of the particular layer, while keeping intact a non-etched layer. A gas mixture may be flowed onto the substrate in separate loops having an oxide layer and an oxynitride layer as an etch layer and a nitride layer as a non-etched layer, for example. A reaction between the resulting gas mixture and the particular layer takes place, resulting in etching of the oxide layer and the oxynitride layer while maintaining the nitride layer in the above example.