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 additionally require to process the backside of the wafer; thus require an accurate alignment between the front and backside of the wafer. 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 [8-9]. In this work, the non-contact infrared alignment system of the Nikon® i-line Stepper NSR-SF150 for both 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 front side resist in resist experiment. After the successful validation of the developed technique, special wafer stacks with FIA alignment marks in the bonding interface are fabricated and exposed. 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 developed technique also allows using significantly smaller alignment marks (i.e. standard FIA alignment marks). Furthermore, the presented method is used, in case of wafer bow related overlay tool problems, for the overlay evaluation of the last two metal layers from production wafers prepared in IHP’s standard 0.25/0.13 µm SiGe:C BiCMOS technology. In conclusion, the exposure and measurement job can be done with the same tool, minimizing the back to front side/interface top layer misalignment which leads to a significant device performance improvement of backside/TSV integrated components and technologies.