The deliberate control over the spatial arrangement of nanostructures is the desired goal for many applications such as, for example, in data storage, plasmonics or sensor arrays. Here we present a novel method to assist the self-assembly process of magnetic nanoparticles. The method makes use of nanostructured aluminum templates obtained after anodization of aluminum discs and the subsequent growth and removal of the newly formed alumina layer, resulting in a regular honeycomb-type array of hexagonally shaped valleys. The iron oxide nanoparticles, 20nm in diameter, are spin-coated onto the surface of honeycomb nanostructured Al templates. Depending on the size, each hexagon site can host up to 30 nanoparticles. These nanoparticles form clusters of different arrangements within the valleys, such as collars, chains and hexagonally closed islands. Ultimately, it is possible to isolate individual nanoparticles. The strengths of the magnetic interaction between particles in a cluster are probed using the memory effect known from the coupled state in superspin glass systems. © 2011 IOP Publishing Ltd.