We report on the self-assembly of Fe adatoms on a Cu(111) surface that is patterned by a metal-organic honeycomb network, formed by coordination of dicarbonitrile pentaphenyl molecules with Cu adatoms. Fe atoms landing on the metal surface are mobile and steered by the quantum confinement of the surface state electrons towards the center of the network hexagonal cavities. In cavities hosting more than one Fe, preferential interatomic distances are observed. The adatoms in each hexagon aggregate into a single cluster upon gentle annealing. These clusters are again centered in the cavities and their size is discerned by their distinct apparent heights. DOI: 10.1103/PhysRevLett.110.086102