We developed a micro-manipulation technique performed under optical microscope observation, which enabled the accurate fabrication of three-dimensional photonic crystals (3D PhCs) for near-infrared light. Thin GaAs plates having an array of rods were picked up with a fine needle by means of the van der Waals force and were mechanically stacked one-by-one by using vertical posts as guides. In spite of the limited spatial resolution in the optical microscope images, the mechanical resolution of the micro-manipulator and the precisely fabricated vertical posts enabled a stacking error that was an order of magnitude smaller than the period of the 3D PhCs. Photoluminescence measurement of a 3D PhC nanocavity containing quantum dots showed a cavity-mode peak in the near-infrared region.