Shallow nanohole structures of uniform size were fabricated on p-type Si by anodizing Si at high applied voltages in a dilute HF solution. The dependence of surface morphology on anodization conditions was investigated and it was found that both HF concentration and ethanol concentration in the electrolyte influenced nanostructures. Nanohole sizes were changed 70–140 nm with increasing applied voltage. Fabricated nanohole structures were used as a substrate for fixing nanoparticles. Nanoparticles, whose sizes were comparable to nanohole sizes, were selectively trapped in nanoholes.