The use of scanning near-field photolithography (SNP) to fabricate DNA nanostructures is described. Two different strategies were employed to generate nanoscale features in oligo(ethylene glycol) (OEG) terminated alkylthiolate self-assembled monolayers (SAMs) on gold. At long exposure times, complete photooxidation of the SAM molecules enabled their displacement by amino-terminated thiol molecules, which were subsequently used to attach ss-DNA molecules; while short exposure times resulted in partial photochemical conversion of the terminal OEG group of the adsorbate to an aldehyde group facilitating the direct attachment of amino-DNA molecules. Arrays of DNA functionalized metal-nanoparticles were then assembled onto the ss-DNA patches through specific DNA hybridization. This methodology provides a facile approach for the assembly of bio-functionalised nanoparticles onto nanofeatures embedded in an inert background and will prove useful in biosensing applications.