Many devices and packaging technologies are built up in a set of several different layers. Many involved materials like Si, III-V semiconductors (i.e. GaAs) and adhesives for temporary bonding and debonding processes become transparent at infrared (IR) wavelengths. IR alignment technologies are used to align embedded structures to a lithography system or to a second substrate in wafer bonding applications using IR illumination. This typically requires a high performance IR source and vision system. Consequently, IR metrology systems are used to verify the overlay of two layers while at least one of them is embedded in a substrate or package using IR technology.