a method and apparatus are provided for performing light - directed reactions in spatially addressable channels within a plurality of channels . one aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels . the reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light - addressable site upstream from the substrate molecules . the method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays , e . g ., oligonucleotides , peptides and carbohydrates , and in the combinatorial synthesis of small molecule arrays for drug discovery .