Methods for controlled isotropic etching of layers of silicon oxide and germanium oxide with atomic scale fidelity are provided. The methods make use of NO activation of an oxide surface. Once activated, a fluorine-containing gas or vapor etches the activated surface. Etching is self-limiting as once the activated surface is removed, etching stops since the fluorine species does not spontaneously react with the un-activated oxide surface. These methods may be used in interconnect pre-clean applications, gate dielectric processing, manufacturing of memory devices, or any other applications where accurate removal of one or multiple atomic layers of material is desired.