Freestanding clean graphene is prepared using graphene samples grown by chemical vapor deposition and direct transfer onto a SiN grid followed by hydrogen plasma treatment. High-resolution transmission electron microscopy has shown that the Au atoms deposited on the graphene possess a unique layer structure with a square arrangement of Au atoms. We found that the Au nanostructure vaporizes under mild electron beam irradiation conditions, which is specific to the unique thin layer structure. (C) 2012 The Japan Society of Applied Physics