Monodisperse Co nanoparticles (NPs), stabilized by organic coating have been synthesized, and their immobilization on a variety of self-assembled monolayers (SAMs) bearing different terminal groups and on SAM-based chemical templates has been studied. The NPs had an average diameter of ∼10 nm and consisted of hcp cobalt covered by a thin (∼1 nm) oxide film. They exhibited pronounced ferromagnetic properties with a blocking temperature above 380 K, which is unusual for the given NP size and is presumably related to the high magnetocrystalline anisotropy associated with the crystallographic perfection of the NPs. The NPs were found to attach selectively to the SAMs bearing the thiol tail group, whereas no stable immobilization to other SAMs, over the electrostatic forces, could be achieved. Finally, based on the results for the individual SAMs, high-contrast 2D structures of the Co NPs were fabricated on SAM-based chemical templates on both micro- and nanometer length scales. The templates were prepared by irradiation-promoted exchange reaction lithography, taking an OH-terminated aliphatic SAMs as the primary template and thiol-bearing aromatic molecules as the substituents.