In this paper, we demonstrate the template-assisted deposition of cetyltrimethylammonium bromide (CTAB) stabilized gold nanorods at lithographically defined positions on a substrate. Overcoating of the nanoparticles with polystyrenesulfonate allows to switch the original nanoparticles positive surface charge to negative and to apply the template-assisted deposition technique developed for citrate-capped gold nanoparticles also to CTAB stabilized nanoparticles. The successful, selective deposition of gold nanorods in trenches with widths down to 50 nm is demonstrated. Our results indicate the potential of this method for the fabrication of well controlled, reproducible plasmonic biosensing substrates, applicable to the vast palette of anisotropic nanoparticle shapes synthesized with CTAB as the templating agent. (C) 2013 Elsevier Inc. All rights reserved.