Chemically synthesized nanostructures such as nanowires 1 , carbon nanotubes 2 and quantum dots 3 possess extraordinary physical, electronic and optical properties that are not found in bulk matter. These characteristics make them attractive candidates for building subsequent generations of novel and superior devices that will find application in areas such as electronics, photonics, energy and biotechnology. In order to realize the full potential of these nanoscale materials, manufacturing techniques that combine the advantages of top-down lithography with bottom-up programmed assembly need to be developed, so that nanostructures can be organized into higher-level devices and systems in a rational manner. However, it is essential that nanostructure assembly occur only at specified locations of the substrate and nowhere else, since otherwise undesirable structures and devices will result. Towards this end, we have developed a hybrid micro/nanoscale-manufacturing paradigm that can be used to program the assembly of nanostructured building blocks at specific, pre-defined locations of a chip in a highly parallel fashion. As a prototype system we have used synthetic DNA molecules and gold nanoparticles modified with complementary DNA strands as the building blocks to demonstrate the highly selective and specific assembly of these nanomaterials on lithographically patterned substrates.