We developed a dry-etching process to form holes with diameters of 5-50 mum in 7-mum thick a-Si/SiO2 three-dimensional (3D) photonic crystal layers fabricated on InP substrates by the autocloning method. We also demonstrated wet-etching processes to remove damaged surfaces of exposed InP substrates and selectively grew In0.62Ga0.38As/In0.45Ga0.31Al0.24As multiple quantum well by molecular beam epitaxy in a region surrounded by a-Si/SiO2 3D photonic crystals. Polarization dependence was observed in a spontaneous emission transmitted at 75 mum in a lateral direction in the photonic crystal layer.