Electronic devices and their highly integrated components formed from semiconductor crystals contain complex three-dimensional (3D) arrangements of elements and wiring. Photonic crystals, being analogous to semiconductor crystals, are expected to require a 3D structure to form successful optoelectronic devices. Here, we report a novel fabrication technology for a semiconductor 3D photonic crystal by uniting integrated circuit processing technology with micromanipulation. Four- to twenty-layered (five periods) crystals, including one with a controlled defect, for infrared wavelengths of 3-4.5 microm, were integrated at predetermined positions on a chip (structural error <50 nm). Numerical calculations revealed that a transmission peak observed at the upper frequency edge of the bandgap originated from the excitation of a resonant guided mode in the defective layers. Despite their importance, detailed discussions on the defective modes of 3D photonic crystals for such short wavelengths have not been reported before. This technology offers great potential for the production of optical wavelength photonic crystal devices.