In this work we present a new approach in physical failure analysis. Fault isolation can be done using volume diagnosis techniques. But when studying the identified defect sites by Focused Ion Beam (FIB) cross-sectioning, correct interpretation of the cross-sectional views strongly relies on choosing an appropriate cutting strategy. However, volume diagnosis techniques do not provide any information on which cutting directions and settings to choose to avoid misinterpretation of the spatial evolution of the defects. The proposed approach is to acquire FIB-SEM tomographic datasets at the defect sites to unequivocally characterize the defects in three-dimensional visualizations, independent of particular cross-sectioning strategies. In this specific case we have applied the methodology at a microcontroller for automotive applications on which a couple of floating VIAS were found. Thanks to the complete information obtained with the tomography, the defect could be assigned to a specific class of etching tools, and the root cause thus be solved.