Selective copper and cobalt deposition on e-beam patterned thiol self-assembled monolayers (SAMs) was studied. Gold electrodes were coated with 1-octadecanethiol (CH3–(CH2)17–SH, ODT) and 1,1′-biphenyl-4-thiol (C6H5–C6H4–SH, BPT) and patterned by e-beam lithography and proximity printing using stencil masks and 300 eV electrons. Electron impact caused ODT-SAMs to lose molecular order and BPT SAMs to cross-link. In both cases the electron induced changes have a distinct influence on the electrochemical properties, which allows selective metal deposition. Selectivity is only achieved within a relatively narrow potential range which depends on the SAM type and the electrolyte. By optimizing the deposition parameters we obtained for copper and cobalt deposition a resolution of about 30 nm for single lines and 50 nm in the fabrication of line gratings. For highest resolution a small proximity effect has to be taken in account.