Near-field optical methods offer unique potential in nanofabrication, because they provide the capacity to initiate highly selective chemical transformations with nanometer scale precision. The basic principles behind scanning near-field photolithography (SNP), in which a scanning near-field optical microscope coupled to a UV laser is used to initiate surface chemical reactions, are described. The fundamental principles underlying the patterning of self-assembled monolayers by SNP are described, and the resolution limits and the basic principles that enable routine achievement of sub-50 nm resolution are discussed. Illustrations are provided of the application of SNP to the patterning of protein molecules on gold surfaces. The patterning of molecular adsorbates on oxide surfaces, including the fabrication of highly miniaturized arrays of DNA on silicon dioxide, is also described. It is argued that SNP holds great promise for the organization of biomolecules on nanometer length scales.