We present chemical modification of self assembled monolayers (SAMs) using electron and ion-beam lithographies. We used thiolated polyethylene oxide (PEO) SAMs on gold to fabricate chemically contrasting patterns at the nanoscale. Patterned surfaces were characterized by X-ray photoelectron spectroscopy (XPS), time of flight-secondary ion mass spectrometry (ToF-SIMS). Results showed a chemical modification of surfaces patterned by means of electron beam (e-beam) lithography and a removal of PEO SAMs on the areas treated with the ion beam. The chemical modification of PEO SAMs converted the non-fouling surfaces on fouling surfaces.