Three-dimensional (3D) photonic crystals with one to four layers of woodpile structures have been fabricated by stacking two-dimensional (2D) photonic plates by micromanipulation. First, air-bridge photonic plates were fabricated as unit structures using conventional IC processing techniques. Then, the 2D photonic plates were stacked using a micromanipulation system. To obtain lattices with precise periodicity, microspheres were inserted into the round openings which were prepared in the frame of the plates. Since neighboring plates have pore openings at the same position, plates were laminated at the proper position automatically. Consequently, positioning error was kept within 50 nm. Optical characteristics of the crystals were evaluated by their reflectance and transmittance at wavenumber between 700 and 7000 cm-1. The formed photonic crystals were expected to have a photonic band gap at around 3030 cm-1. As the number of layers was increased, the reflectance at around 3030 cm-1 increased to 60 %, and the transmittance at the same wavelength region decreased to 30 %.