In this study, a novel technique was introduced for selective surface modification of amine-functionalized magnetic nanoparticles. The method was based on alignment of magnetic nanoparticles in an external magnetic field, which resulted in formation of chain-like assemblies in diluted suspensions. The aligned chains were then modified on the surface via reaction of isocyanate species with the particle functionalities. Finally, after removal from the reactor medium, particles with segmented distribution of surface functionalities were achieved. We named these partially blocked amine-functionalized magnetic nanoparticles as "Saturn" nanoparticles. Application of the particles in fabrication of magnetic assemblies was successfully demonstrated. Using methylene diphenyl diisocyanate (MDI) as the bridging agent, structures in different forms such as chains and filaments were produced by the Saturn particles and compared with cross-linked structures of the unmodified amine-functionalized particles. It is expected that this novel nanoparticle with its unique structure will have great potential in assembly fabrication with a variety of applications in biomedical fields.