A critical shortcoming of current surface functionalization schemes is their inability to selectively coat patterned substrates at micrometer and nanometer scales. This limitation prevents localized deposition of macromolecules at high densities, thereby restricting the versatility of the surface. A new approach for functionalizing lithographically patterned substrates that eliminates the need for alignment and, thus, is scalable to any dimension is reported. We show, for the first time, that electropolymerization of derivatized phenols can functionalize patterned surfaces with amine, aldehyde, and carboxylic acid groups and demonstrate that these derivatized groups can covalently bind molecular targets, including proteins and DNA. With this approach, electrically conducting and semiconducting materials in any lithographically realizable geometry can be selectively functionalized, allowing for the sequential deposition of a myriad of chemical or biochemical species of interest at high density to a surface with minimal cross-contamination.