The etching of graphite surfaces by two different types of oxidative treatments, namely dielectric barrier discharge (DBD) air plasma and ultraviolet-generated ozone (UVO), has been investigated and compared by means of scanning tunneling microscopy (STM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). Although the attack is initiated in both cases with the formation of individual, isolated atomic-scale defects (in particular, atomic vacancies), its subsequent evolution indicated that different mechanisms drive the surface modification in the two types of treatment, which greatly differ in etching selectivity. Thus, physical processes (i.e., ion bombardment) dominate the attack by DBD air plasma, which are not present in the case of UVO oxidation. The effects of the different etching mechanisms on the graphite surface structure, as visualized by STM down to the atomic scale, are discussed and found to be consistent with the Raman spectroscopy and XPS data. This type of information can be relevant when selecting the most appropriate type of surface modification of carbon materials for specific purposes.