Micrometer-sized oxidation patterns were created in chemical vapor deposition grown multilayered, non-Bernal stacked graphene through scanning probe lithography. The oxidized patterns were then reduced by irradiation using a focused X-ray beam. The topographical, structural, and chemical modifications of the oxidized graphene were characterized through atomic force microscopy, micro-Raman spectroscopy, and micro-X-ray photoelectron spectroscopy, respectively, before and after reduction of the oxidized patterns. For multilayered graphene (MLG), we found that oxidation only occurs for the first outermost layer. Furthermore, it was found that while the oxygen functional groups were almost completely removed by the reduction process, the restoration to a two-dimensional honeycomb structure of the reduced graphene was dependent on the number of layers. Notably, structural restoration is more effective for MLG, as compared to the single-layered counterpart. The mechanism of structural restoration is discussed in the light of solid-phase epitaxial regrowth.