Regularly sized Fe and Co nanostructures are created using two-dimensional metal-organic honeycomb lattices as templates. They consist of dicarbonitrile-polyphenyl molecules coordinated to Co centers on Ag(111). Subsequently deposited Fe or Co atoms nucleate clusters at specific sites on top of the metal-organic lattices while leaving their hexagonal pores empty. Choosing the deposition temperature, one can selectively decorate the molecules (120 K ) or the Co coordination nodes (190 K ) with Fe. The distance between the Fe and Co clusters and their shape can be adjusted through the lattice constant of the template by varying the number of phenyl rings in the molecules.