The ability to organize nanomaterials, e.g., Au nanoparticles (NPs) and graphene oxide (GO) sheets, into ordered structures with high accuracy and resolution on a substrate is crucially important for fundamental studies and applications. In this letter, we developed a simple and efficient method to generate positively charged 11-amino-1-undecanethiol (AUT) templates on An substrates, which were successfully used for controlled assembly of negatively charged Au NPs or GO sheets from aqueous solution. The templates were obtained by passivation of the exposed An area with AUT after 16-mercaptohexadecanoic acid (MHA) patterns were generated by dip-pen nanolithography (DPN) on Au. The electrostatic interaction ensures that the Au NPs and GO sheets only adsorb on the designed AUT areas. Importantly, by using this method, the number of ALL NPs adsorbed on patterned areas can be controlled, and a single Au NP array was successfully achieved.