The directed placement of Cu nanostructures on surfaces has been studied using a combination of scanning probe lithography and electroless metal deposition onto nanopatterned SAMs of 16-mercaptohexadecanoic acid (16-MHA) on Au. In situ studies using nanoscale molecular gradients reveal how controlling the areal density of the 16-MHA molecules dictates the nucleation and growth of the metal nanostructures. The influence of controlling pattern line spacing and tip path on pattern feature fidelity is also discussed.