The precise, size-selective assembly of nanoparticles gives rise to many applications where the assembly of nano building blocks with different biological or chemical functionalizations is necessary. We introduce a simple, fast, reproducible-directed assembly technique that enables a complete sorting of nanoparticles with single-particle resolution. Nanoparticles are size-selectively assembled into prefabricated via arrays using a sequential template-directed electrophoretic assembly method. Polystyrene latex (PSL) nanoparticles with diameters ranging from 200 to 50 nm are selectively assembled into vias comparable to nanoparticle diameter. We investigate the effects of particle size and via size on the sorting efficiency. We show that complete sorting can be achieved when the size of the vias is close to the diameter of the nanoparticles and the size distribution of the chosen nanoparticles does not overlap. The results also show that it is necessary to keep the electric field on during the insertion and removal of the template. To elucidate the versatility and nil effects that the electrophoresis assembly technique has on the assembled nanoparticle characteristics, we have assembled cancer-specific monoclonal antibody-2C5-coated nanoparticles and have also shown that they can successfully measure low concentrations of the nucleosome (NS) antigen.