The organization of metallic nanoparticles (NPs) into ordered arrays on nanopatterned surfaces is an enabling process to fabricate devices and study the properties of the particles. Tailoring the interaction between NPs and nanopatterns is a necessity to gain a high level of control in this process. Here, nanopatterned poly(ethylene glycol) (PEG) brushes are presented as a platform for the organization of Au NPs on surfaces. The binding of citrate-stabilized Au NPs to the PEG brushes depends on the size of the particles and molecular weight of the brushes: the density of NPs immobilized on the nanopatterns of PEG brushes increases with decreasing the diameter of the particles and increasing the chain length of the brushes. The key aspect of the process is to pattern PEG brushes with high resolution and chemical contrast to provide controllable and specific interaction between Au NPs and nanopatterns at a single particle resolution. The modulation of the number (0–4) of Au NPs (e.g., 30 nm) per patterned feature with a high level of accuracy and the generation of patterned heterostructures that consist of two different sizes (e.g., 40 and 20 nm) of particles constitute two examples showing the capabilities of the presented platform.