In the last decades the semiconductor technology has been driven by Moore’s law leading to high performance CMOS technologies with feature sizes of less than 10 nm . It has been pointed out that not only scaling but also the integration of novel components and technology modules into CMOS/BiCMOS technologies is becoming more attractive to realize smart and miniaturized systems . Driven by new applications in the area of communication, health and automation, new components and technology modules such as BiCMOS embedded RF-MEMS, high-Q passives, Sibased microfluidics and InP-SiGe BiCMOS heterointegration have been demonstrated [3-6]. In contrast to standard VLSI processes fabricated on front side of the silicon wafer, these new technology modules require addition backside processing of the wafer; thus an accurate alignment between the front and backside of the wafer is mandatory. In previous work an advanced back to front side alignment technique and implementation into IHP’s 0.25/0.13 μm high performance SiGe:C BiCMOS backside process module has been presented . The developed technique enables a high resolution and accurate lithography on the backside of BiCMOS wafer for additional backside processing. In addition to the aforementioned back side process technologies, new applications like Through-Silicon Vias (TSV) for interposers and advanced substrate technologies for 3D heterogeneous integration demand not only single wafer fabrication but also processing of wafer stacks provided by temporary and permanent wafer bonding . Therefore, the available overlay measurement techniques are not suitable if overlay and alignment marks are realized at the bonding interface of a wafer stack which consists of both a silicon device and a silicon carrier wafer. The former used EVG 40NT automated overlay measurement system, which use two opposite positioned microscopes inspecting simultaneous the wafer back and front side, is not capable measuring embedded overlay marks. In this work, the non-contact infrared alignment system of the Nikon i-line Stepper NSR-SF150 for both the alignment and the overlay determination of bonded wafer stacks with embedded alignment marks are used to achieve an accurate alignment between the different wafer sides. The embedded field image alignment (FIA) marks of the interface and the device wafer top layer are measured in a single measurement job. By taking the offsets between all different FIA’s into account, after correcting the wafer rotation induced FIA position errors, hence an overlay for the stacked wafers can be determined. The developed approach has been validated by a standard back to front side application. The overlay was measured and determined using both, the EVG NT40 automated measurement system with special overlay marks and the measurement of the FIA marks of the front and back side layer. A comparison of both results shows mismatches in x and y translations smaller than 200 nm, which is relatively small compared to the overlay tolerances of ±500 nm for the back to front side process. After the successful validation of the developed technique, special wafer stacks with FIA alignment marks in the bonding interface are fabricated. Due to the super IR light transparency of both doubled side polished wafers, the embedded FIA marks generate a stable and clear signal for accurate x and y wafer coordinate positioning. The FIA marks of the device wafer top layer were measured under standard condition in a developed photoresist mask without IR illumination. Following overlay calculation shows an overlay of less than 200 nm, which enables very accurate process condition for highly scaled TSV integration and advanced substrate integration into IHP’s 0.25/0.13 μm SiGe:C BiCMOS technology. The presented method can be applied for both the standard back to front side process technologies and also new temporary and permanent wafer bonding applications.