In this work, covalent modification of mono- and bilayer graphene is achieved using tetrafluoromethane (CF₄), oxygen and hydrogen RF plasma. Controlled modification of graphene is usually difficult to achieve, in particular with oxygen plasma, which is rather aggressive and usually leads to etching of graphene. Here we use x-ray photoelectron spectroscopy and Raman spectroscopy to show that mild plasma conditions and fine tuning of the number of functional groups can be obtained in all plasmas by varying parameters such as exposure time and sample position inside the chamber. We found that even for the usual harsh oxygen treatment the defect density could be lowered, down to one defect for 3.5 × 10⁴ carbon atoms. Furthermore, we show that CF₄ plasma leads to functionalization without etching and that graphene becomes an insulator at saturation coverage. In addition, the reactivity of mono- and bilayer graphene was studied revealing faster modification of monolayer in oxygen and CF₄ plasma, in agreement with previous works. In contrast, similar modification rates were observed for both mono- and bilayer during hydrogenation. We attribute this discrepancy to the presence of more energetic species in the hydrogen plasma such as positive ions that could play a role in the functionalization process.