The present invention provides a functionalized nanosubstrate or "nanotemplate" that is useful for selectively assembling nanoelements across a large area. The nanotemplate is capable of guiding the massive parallel assembly of nanoelements to fabricate a three-dimensional nanostructure. Nanoelements can also be transferred at a high-rate from the template to a recipient substrate. Examples of these nanoelements include, but are not limited to, carbon nanotubes, nanocrystals, dendrimers, nanoparticles, nanowires, biological materials, proteins, molecules and organic nanotubes. The invention also provides a nanotemplate combined with selectively assembled nanoelements. The invention encompasses methods for functionalizing a nanosubstrate. These methods involve providing a substrate having a known topology and polymerizing a monomer on its surface. Methods for selecting nanoelements and guiding their self-assembly are also disclosed. The invention further provides a method for modifying and transferring assembled nanoelements to a recipient substrate.