A simple and efficient method of thinning graphene with an accuracy of a single layer is proposed, which includes mild nitrogen plasma irradiation and annealing in Ar/O2. On the basis of our data, plasma irradiation induces damages in the top-layer graphene and the annealing removes the damaged layer by fast oxidation. The process was used to turn bilayer graphene into monolayer as well as thin multilayer graphene layer-by-layer via repeated utilization. Combined with electron beam lithography, patterns were fabricated by selectively removing graphene planes. The thinned graphene possesses good quality verified by atomic force microscopic investigation and Raman analysis. The process presented here offers a very useful post-synthesis manipulation of graphene thickness, which may find important applications for graphene-based device fabrication.