Methods for selectively depositing nanostructures on a support layer include contacting the support layer with functionalized catalyst particles. The functionalized catalyst particles can form a self-assembled monolayer of catalyst particles on the support layer and the functionalized catalyst particles can be used to catalyze nanostructure growth. In one embodiment of the disclosed method, zinc oxide nanowires are grown on a patterned substrate using functionalized gold nanoparticles. Patterned arrays of self-assembled nanostructures and nanoscale devices using such nanostructure arrays are also described.