Molecular self-assembly films are expected to tailor the surface process by the periodic nanostructures and add-on functional groups. In this work, a molecular network of melamine with featured pores of subnanometer size is prepared on the Au(111) surface, and is found to be able to trap the gold adatoms and concomitant single vacancies generated under the impingement of CO molecules at room temperature. DFT calculations suggest that the strong CO-Au adatom interaction as well as the high adhesion of the Au adatom inside the melamine pore could well be the driving force behind such process. This study not only sheds light onto the interactions between gasses and the metal surface that is covered by molecular self-assembly films, but also provides a novel route to manipulate the monoatomic surface species which is of catalytic interest.