A 3 keV low-energy proton beam was used to irradiate a silicon substrate for selective modification. The water contact angle measurement, chemical etching test with HF and the auger electron spectroscopy were used to investigate the chemical properties and the material composition of the proton beam-irradiated silicon substrate. The proton beam-irradiated silicon substrate was covered with a silicon oxide layer of about 60-70 angstroms due to the incorporation of oxygen molecules after exposure to ambient air. The silicon oxide layer produced by the proton beam was highly resistant to HF treatment which typically used to remove the silicon oxide on a substrate, and the surface of it was more hydrophilic than the native silicon oxide removed silicon surface with Si-H surface group. For the selective growth of carbon nanotubes (CNTs), the silicon oxide pattern was easily fabricated via proton beam irradiation when the silicon substrate was covered with a shadow mask. The Fe-Mo bimetallic catalysts for the growth of CNTs were adsorbed onto the silicon oxide layer, which is more hydrophilic than the silicon surface. The CNTs were grown on the patterned substrate using a chemical vapor deposition method, and it was confirmed by scanning electron microscopy.