We present a method for improving ferntomole-level trace detection (10(9) molecules) using large-area surface-enhanced Raman scattering (SERS) substrates. Using multiphoton-induced exposure of a commercial. photoresist, we physically limit the available molecular adsorption sites to only the electromagnetic "hot spots" on the substrate. This process prevents molecules from adsorbing to sites of weak SERS enhancement, while permitting adsorption to sites of extraordinary SERS enhancement. For a randomly adsorbed submonolayer of benzenethiol molecules the average Raman scattering cross section of the processed sample is 27 times large than that of an unprocessed SERS substrate.