Self-assembly guided by molecular recognition has in the past been employed to assemble nanoparticle superstructures like hypercrystals or nanoparticle molecules. An alternative approach, the direct molecule-by-molecule assembly of nanoscale superstructures, was demonstrated recently. Here we present a hybrid approach where we first assemble a pattern of binding sites one-by-one at a surface and then allow different nanoparticles to attach by self-assembly. For this approach, biotin bearing DNA oligomers were picked up from a depot using a cDNA strand bound to an AFM tip. These units were deposited in the target area by hybridization, forming a recognition pattern on this surface. Fluorescent semiconductor nanoparticles conjugated with streptavidin were allowed to assemble on this scaffold and to form the final nanoparticle superstructures.