Abstract 3D integration takes more and more importance in the microelectronics industry. This paper focuses on two types or objects, which are copper pillars (25 micrometer of diameter) and hybrid bonding samples. It aims at a statistical morphology observation of hybrid bonding structures, which underwent an electromigration test at 350 deg C and 20 mA. The goal of the study is two-fold. It is both to limit the overall time needed to perform a whole process flow, from sample preparation to reconstructed volume, and to limit the time of human intervention. To achieve this goal, three strategies are presented: improving the sample preparation scheme, reducing the number of projections with iterative algorithms and the Structural SIMilarity function, and automating the post-processing. The post-processing of the data is fully automated and directly renders the reconstructed volume. The high signal to noise ratio allows for further segmentation and analysis.