We develop a plasma processing technique for modifying the surface properties of micro- and nanostructured materials for biomedical applications. We also investigate the physical and chemical roles of the plasma in modifying the surfaces of micro- and nanostructured materials such as magnetic nanoparticles (MNPs), carbon nanotubes (CNTs), nanophosphors, and biomolecules for various biomedical applications. We introduced amino groups onto the surfaces of graphite-encapsulated iron compound nanoparticles using a low-pressure Ar plasma pre-treatment and ammonia plasma post-treatment followed by immobilization of biomolecules, such as dextran and N-acetyllactosamine (LacNAc). The present technique was also used to introduce amino groups onto CNT dot arrays grown on Si substrates for use in biochip sensors.