Regularly arranged magnetic out-of-plane patterns in continuous and flat films are promising for applications in data storage technology (bit patterned media) or transport of individual magnetic particles. Whereas topographic magnetic structures are fabricated by standard lithographical techniques, the fabrication of regularly arranged artificial domains in topographically flat films is difficult, since the free energy minimization determines the existence, shape, and regularity of domains. Here we show that keV He(+) ion bombardment of Au/Co/Au layer systems through a colloidal mask of hexagonally arranged spherical polystyrene beads enables magnetic patterning of regularly arranged cylindrical magnetic monodomains with out-of-plane magnetization embedded in a ferromagnetic matrix with easy-plane anisotropy. This colloidal domain lithography creates artificial domains via periodic lateral anisotropy variations induced by periodic defect density modulations. Magnetization reversal of the layer system observed by magnetic force microscopy shows individual disc switching indicating monodomain states.