We present a new strategy to fabricate a monolayer assembly of Br-terminated Co nanoparticles on functionalized Si surfaces by using chemical covalent bonding and microcontact printing method. Self-assembled monolayers (SAMs) of the Co nanoparticles formed on the hydroxyl-terminated Si surface exhibit two-dimensional island networks with locally ordered arrays via covalent linkage between nanoparticles and surface. On the other hand, SAMs of the nanoparticles on the aminopropyl-terminated Si surface show an individual and random distribution over an entire surface. Furthermore, we have fabricated striped architectures of Co nanoparticles using a combination of microcontact printing and covalent linkage. Microcontact printing of octadecyltrichlorosilane and selective covalent linkage between nanoparticles and functionalized Si surfaces lead to a hybrid nanostructure with selectively assembled nanoparticles stripes on the patterned functionalized Si surfaces.