An efficient approach for the controlled production of artificial structural defects in the topmost graphitic layer is proposed. For the surface morphology modification, the Ar+ ion sputtering with retarding field applied to the sample followed by vacuum or oxygen annealing is used. The procedure can be carried out in a standard ultrahigh vacuum set-up; no special design equipment is required. Proposed approach allows surface modification at the atomic level. Surface structures forming at each step of the procedure look promising for the deposited metal particles immobilization and stabilization towards thermal sintering.