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Functionalized graphene is a versatile material that has well-known physical and chemical properties depending on functional groups and their coverage. However, selective control of functional groups on the nanoscale is hardly achievable by conventional methods utilizing chemical modifications. We demonstrate electrical control of nanoscale functionalization of graphene with the desired chemical coverage of a selective functional group by atomic force microscopy (AFM) lithography and their full recovery through moderate thermal treatments. Surprisingly, our controlled coverage of functional groups can reach 94.9% for oxygen and 49.0% for hydrogen, respectively, well beyond those achieved by conventional methods. This coverage is almost at the theoretical maximum, which is verified through scanning photoelectron microscope measurements as well as first-principles calculations. We believe that the present method is now ready to realize 'chemical pencil drawing' of atomically defined circuit devices on top of a monolayer of graphene. © 2014 Nature Publishing Group All rights reserved.