As packaging drives to extend the capabilities of Moore’s Law via heterogenous integration, numerous bonding technologies have emerged as potential pathways, allowing for integration of both a variety of devices in the lateral space as well as vertical integration of chips via stacking. As vertical integration on interposer becomes more complex due to shrinking CDs and increasing die layers, alignment and shape control in the bonding process becomes critical. Thermocompression bonding (TCB) is particularly well-suited for larger die, where localized reflow allows a better control of chip gap height and tilt throughout the bonding process. TCB systems require both high accuracy and repeatability in all dimensions to provide a reliable system in package. While a 2D system can provide a plan view assessment of a single bond layer between two chips, it falls short in characterizing the critical z-dimension in a highly integrated chip stacking scenario. Therefore a robust solution is needed for both system alignment validation in the x,y plane as well as a capability to explore gap height and bump quality/buried issues in high aspect ratio TSV. This paper will explore an x-ray application of a stacked 15-layer die-to-interposer structure to qualitatively validate overall health of the TSV (bond, pad, fill) via a nondestructive volumetric method as well as quantitatively evaluate stacked die for via/ball/pad alignment to determine overall alignment shift during the bonding process. In the test vehicle for a flip chip FO-WLP process flow first presented by IMEC, a silicon (Si) bridge is utilized to connect the logic and through-package via dies with a bump pitch of 20µm for the logic die interconnect. This is done by carefully aligning the logic dies on the carrier and then placing the through-package dies aligned to the carrier and logic dies. In the final step, a high accuracy placement and stacking TCB tool attaches the Si bridge. To perform an accurate assessment for bump alignment and bond quality, an initial high-resolution 3D x-ray scan is performed on a 1.5mm3 region of interest with over 2,000 individual projections at a 1.4µm voxel resolution with a 4x objective, taking approximately two hours. The dataset is put through a deep-learning algorithm which generates an AI model. This model is then applied to a faster scan of 15 minutes with a 1.4µm voxel resolution for the same field of view (FOV) on a nearby array and the data is collected and processed. To verify alignment of the entire sample, data is collected on the tightest pitch (in this case 20µm) oriented in both the vertical (x) and horizontal (y) plane in the through-silicon via (TSV) region. The z-plane is analyzed and processed by computer vision algorithms, and individual interconnects are then quantified and sorted for solder height (z), width (x,y) and TSV misalignment (deviation from expected center, x1y1 → x2y2). To validate the model, a high-resolution uncorrected 20h scan and a 15min scan based on deep learning are collected for the same region of interest (ROI). The data is comparable. Furthermore, the global misalignment data between both datasets demonstrates similar misalignment propagating through the 15-layer stack.