Residual impurities on the surface of graphene after device fabrication degrade the performance of graphene electronic devices. It is important to solve this issue in order to use graphene in electronic devices. In this study, we removed residues using four plasma treatment methods following the photolithography process. The four plasma treatment methods were hydrogen plasma treatment (Process 1, P-1), methane plasma treatment (Process 2, P-2), hydrogen plasma pre- and methane plasma post-treatment (Process 3, P-3), and hydrogen-methane mixed plasma treatment (Process 4, P-4). The results were analyzed using atomic force microscopy and Raman spectroscopy. Of the four treatments, Process 4 showed the most remarkable removal of photoresist residue and healing of the damaged graphene film, thereby improving the mobility of the graphene. The total resistance of the graphene channel in the device was also considerably reduced. These results reveal that a hydrogen-methane mixed plasma treatment (P-4) could be a powerful method for removing residue on the surface of graphene after the lithography process.