Methods of and apparatuses for processing substrates having carbon-containing material using atomic layer deposition and selective deposition are provided. Methods involve exposing a carbon-containing material on a substrate to an oxidant and igniting a first plasma at a first bias power to modify a surface of the substrate and exposing the modified surface to an inert plasma at a second bias power to remove the modified surface. Methods also involve selectively depositing a second carbon-containing material onto the substrate. ALE and selective deposition may be performed without breaking vacuum.