A process for etching multiple layers on a substrate 25 in an etching chamber 30 and cleaning a multilayer etchant residue formed on the surfaces of the walls 45 and components of the etching chamber 30. In multiple etching steps, process gas comprising different compositions of etchant gas is used to etch layers on the substrate 25 thereby depositing a compositionally variant etchant residue inside the chamber 30. In one cleaning step, a first cleaning gas is added to the process gas to clean a first residue or to suppress deposition of the first residue onto the chamber surfaces. In a second cleaning step, another residue composition is cleaned off the chamber surfaces using a second cleaning gas composition.