We demonstrate the three-dimensional arrangement of silica microparticles in body-centered cubic lattice structure using both a relief pattern formed in the film of the azopolymer and silica micro particles dispersed in a nematic liquid crystal. In the method, firstly, the square lattice relief structures with the spacing of 2000 nm and the depth of 400 nm were formed on the azopolymer film by twice exposure to two beam interference patterns with coherent light of 488 nm in wavelength from Ar ion laser. Next, a nematic liquid crystal (5CB) containing 2000 nm diam. silica microparticles, with the surface modified with silane coupling reagent giving rise to homeotropic texture, was dropped on the relief structure on the azopolymer. The two dimensional square lattice structures of the micropaticles were formed spontaneously in an isotropic to nematic phase transition. Finally, the microparticles were three-dimensionally arranged by using optical tweezers. The microparticles were successfully stacked in a four-step pyramid structure with body centered tetragonal lattice structure.