The present invention provides methods and tools for directed assembly of nanoelements across a large area using a nanosubstrate. The nanosubstrate has a substrate layer, an adhesive layer, a conductive layer, and an insulating layer that is interrupted by one or more nanotrenches or nanowells having a width of at least 20 nm. The nanosubstrate allows the rapid assembly of linear assemblies and arrays of single walled carbon nanotubes and nanoparticles by DC electrophoresis. The density of nanoelements assembled can be controlled by varying the voltage and trench size. Functionalized nanoparticles can be assembled into arrays useful, e.g., as biosensors.