Conventional soft-lithography methods involving the transfer of molecular "inks" from polymeric stamps to substrates often encounter micrometer-scale resolution limits due to diffusion of the transferred molecules during printing. We report a "subtractive" stamping process in which silicone rubber stamps, activated by oxygen plasma, selectively remove hydroxyl-terminated alkanethiols from self-assembled monolayers (SAMs) on gold surfaces with high pattern fidelity. The covalent interactions formed at the stamp-substrate interface are sufficiently strong to remove not only alkanethiol molecules but also gold atoms from the substrate. A variety of high-resolution patterned features were fabricated, and stamps were cleaned and reused many times without feature deterioration. The remaining SAM acted as a resist for etching exposed gold features. Monolayer backfilling into the lift-off areas enabled patterned protein capture, and 40-nanometer chemical patterns were achieved.