Current development trends concerning miniaturizing of electronics and photonics systems are aiming at assembly and 3D co-integration of a broad range of technologies including MEMS, microfluidics, wafer level optics, and silicon photonics. To this end, on-chip integration using silicon-photonics platform offers a wide range of possibilities addressing passive optics functionality, active optoelectronic devices, and compatibility with CMOS fabrication. On the other hand, the hybrid technology enabling volume manufacturing of such systemon-chip components it is still in an early development stage. Here, a new type of machine vision system enabling precision stacking and bonding processes of III-V components on silicon photonics chips is introduced. In particular, we focus on the ability to see through substrates with high resolution, which is crucial for the alignment of the markers used for assembly of integrated components on silicon wafer. The system is based on the use of a black silicon enhanced CMOS sensor with extended wavelength response beyond transparency cut off wavelength for silicon substrate. We study the use of the camera system as a microscope with bottom coaxial infrared illumination scheme and demonstrate the ability of through-silicon vision for one-and twolayered silicon photonic integrated circuit samples. The ability of observing objects with dimensions down to 2 µm is confirmed. This resolution is close to diffraction limit and corresponds to the dimensions of optical waveguide structures on the photonic integrated circuits surface. In addition, we demonstrate the implementation of a two-dimensional Fourier transform based autofocusing technique for through-silicon IR microscopy. These building blocks offer a solution for advanced photonic integration processes and other through-silicon vision related applications, which is instrumental for a large variety of assembly, lithography, and wafer bonding setups.