Methods for accurate and conformal removal of atomic layers of materials make use of the self-limiting nature of adsorption of at least one reactant on the substrate surface. In certain embodiments, a first reactant is introduced to the substrate in step (a) and is adsorbed on the substrate surface until the surface is partially or fully saturated. A second reactant is then added in step (b), reacting with the adsorbed layer of the first reactant to form an etchant. The amount of an etchant, and, consequently, the amount of etched material is limited by the amount of adsorbed first reactant. By repeating steps (a) and (b), controlled atomic-scale etching of material is achieved. These methods may be used in interconnect pre-clean applications, gate dielectric processing, manufacturing of memory devices, or any other applications where removal of one or multiple atomic layers of material is desired.