Methods of and apparatuses for processing substrates having carbon-containing material using atomic layer etch and selective deposition are provided. Methods involve exposing a carbon-containing material on a substrate to an oxidant and igniting a first plasma to modify a surface of the substrate and exposing the modified surface to a second plasma at a bias power to remove the modified surface. Methods also involve selectively depositing a second carbon-containing material onto the substrate using a precursor having a chemical formula of CxHy, where x and y are integers greater than or equal to 1. ALE and selective deposition may be performed without breaking vacuum.