Mesoporous silica films were prepared on glass plates by a dip coating method, and the film/plate samples were used as a support for Au, Pt and Pd nanoparticles. By H-2- or photo-reduction of metal precursors impregnated on the films, metal nanoparticles are formed with an ordered array structure in the mesopores. The nanoparticles are isolated by dissolving the silica film with a dilute HF solution, and the particles are stabilized with ligands such as 1-dodecanethiol and triphenylphosphine. The diameter of the separated nanoparticles is 2.5 nm with narrow distributions, showing that uniform particles are formed in the mesopores. Selective formation of metal nanoparticles rather than nanowires suggests that a 3D-hexagonal structure is involved in the 2D-hexagonal mesoporous silica films. To study the formation of nanoparticles in a 3D-hexagonal structure, HMM-2 powder was used as a support, and in fact Au and Pt nanoparticles are formed in the HMM-2 powders. The XRD study suggests that the Au nanoparticles in the film/plate have an anisotropic orientation in the mesoporous channels. The Au/film/plate sample gives a weak plasmon peak at 570-580 nm using diffuse-reflectance UV-visible spectroscopy, which is shifted to high wavelength by 50-60 nm compared with larger Au particles.