Protective caps residing at an interface between copper lines and dielectric diffusion barrier layers are used to improve various performance characteristics of interconnects. The caps, such as cobalt-containing caps or manganese-containing caps, are selectively deposited onto exposed copper lines in a presence of exposed dielectric using CVD or ALD methods. The deposition of the capping material is affected by the presence of carbon-containing contaminants on the surface of copper, which may lead to poor or uneven growth of the capping layer. A method of removing carbon-containing contaminants from the copper surface prior to deposition of caps involves contacting the substrate containing the exposed copper surface with a silylating agent at a first temperature to form a layer of reacted silylating agent on the copper surface, followed by heating the substrate at a higher temperature to release the reacted silylating agent from the copper surface.