We show that 4'-nitro-1,1'-biphenyl-4-thiol self assembled monolayers (NBPT SAMs) on gold can be exchanged with 11-(mercaptoundecyl)triethylene glycol (C(11)EG(3)OH) SAMs via vapor deposition (VD). The pristine and the exchanged SAMs obtained by VD as well as solution method (SM) were characterized by X-ray photoelectron spectroscopy (XPS) and polarization modulation infrared reflection absorption spectroscopy (PMIRRAS). Using surface plasmon resonance (SPR), it is shown that C(11)EG(3)OH SAMs on gold obtained by vapor deposition exchange (VIDE.) have the same protein resistivity as SAMs obtained by the direct self-assembly process. As expected, the cross-linked NBPT SAM are found to be resistive to both exchange processes, VDEx and solution method exchange (SME.). In this way, VDEx opens up an elegant and new approach of patterning SAM surfaces in situ at vacuum conditions without using any solvents. By combining electron irradiation-induced chemical lithography of NBPT SAMs with VDEx biofunctional patterned substrates were engineered and used for immobilization of pidtein arrays.