Disclosed are partially deactivated metal catalysts useful for modifying structures of nanomaterials. The present invention is also directed to a method for preparing the partially deactivated metal catalysts, which comprises patterning a substrate with micelles containing iron nanoparticles, removing the micelles from the patterned substrate to deposit the iron nanoparticles thereon, nitriding the iron nanoparticles using a nitrogen plasma, and exposing the nitrided iron nanoparticles to a mixture of ethanol and nitric acid to remove iron from the surface of the nitrided nanoparticles. The iron nitride metal catalyst with a nano-size according to the present invention comprises a core that includes deactivated iron nitride and an active shell surrounding the core. Thus, when preparing a carbon nanotube, the metal catalyst can be effectively used to control the number of walls formed in the carbon nanotube.