A novel nanopatterning process was developed by combining capillary force lithography (CFL) and microcontact printing (µCP). Flat polydimethylsiloxane (PDMS) was used as the substrate in CFL, and after chemical functionalization, as the stamp in µCP, which increased the resolution of both methods. The polymer patterns, produced by CFL on a thin polymer film on the flat PDMS substrate, acted as a mask to oxidize the uncovered regions of the PDMS. The chemical patterns were subsequently formed by gas phase evaporation of a fluorinated silane. After removal of the polymer, these stamps were used to transfer thiol inks to a gold substrate by µCP. Gold patterns at a scale of less than 100 nm were successfully replicated by these chemically patterned flat PDMS stamps.