The integration of top-down (lithographic) and bottom-up (synthetic) methods remains one of the outstanding challenges in molecular nanoscience. There are no established tools for the manipulation of surface chemical structure in the length range from ca. 100 nm to the dimensions of a single biomacromolecule. Scanning near-field photolithography (SNP), in which a scanning near-field optical microscope coupled to a UV laser is employed as a light source, may be used to execute specific molecular transformations with a spatial resolution of a few tens of nm and, at best, 9 nm (ca. λ/30). Several strategies will be described for the patterning of proteins and nucleic acids on metal and oxide surfaces. We demonstrate two approaches. First, photodegradation of oligo(ethylene glycol) (OEG) functionalised surfaces provides a simple route to the covalent attachment of proteins to non-fouling surfaces. Photodegradation of OEG-terminated thiols provides a simple, one-step route to the conversion of a protein-resistant surface to a protein-binding one. Similar methodologies may be extended to oxide surfaces, through the formation of OEG-functionalised siloxane films. Photodegradation yields aldehyde functionalities, to which nitrilo triacetic acid (NTA) functionalised amines may be coupled, and subsequently dertivatised, following nickel complexation, with histidine-tagged proteins, providing a facile route to the site-specific immobilisation of proteins on glass. Second, siloxane monolayers offer fruitful opportunities for the incorporation of synthetic chemical methods into nanolithography. Halogenated monolayers may be converted to aldehydes or to carboxylic acids, by controlling the exposure. Alternatively, 2-nitrophenylpropyloxycarbonyl (NPPOC) protected aminosiloxane monolayers on glass may be selectively deprotected by SNP, yielding amine groups for further functionalisation with very high spatial resolution. The synthetic flexibility and versatility of photochemical methods, when combined with near-field methods for control of exposure, offers enormous potential for integrating top-down and bottom-up methods.