Photonic integrated circuits (PICs) enable manipulation of light on a chip for telecommunications and information processing. They can be made with silicon and silicon-compatible materials using complementary metal-oxide-semiconductor (CMOS) fabrication techniques developed for making electronics. Unfortunately, most light sources are made with III-V and II-VI materials, which are not compatible with silicon CMOS fabrication techniques. As a result, the light source for a PIC is either off-chip or integrated onto the PIC after CMOS fabrication is over. Hybrid integration can be improved by forming a recess in the PIC to receive a III-V or II-VI photonic chip. Mechanical stops formed in or next to the recess during fabrication align the photonic chip vertically to the PIC. Fiducials on the PIC and the photonic chip enable sub-micron lateral alignment. As a result, the photonic chip can be flip-chip bonded to the PIC with sub-micron vertical and lateral alignment precision.