Abstract This paper presents two case studies, based on 32nm Silicon-On-Insulator (SOI) and 28nm bulk Si technology, on finding the root cause of nanometer scale short failures using Passive Voltage Contrast (PVC), Active Voltage Contrast (AVC) and Transmission Electron Microscopy (TEM). PVC/AVC is used as precision localization technique that is critical for a successful FA-TEM analysis. Combining planar TEM sample preparation and high sensitivity Energy Dispersive Spectroscopy (EDS) mapping, a small residual filament, which is not visible even at high resolution TEM, is found to short two metal lines. The effective usage of voltage contrast and TEM provides the need of high throughput, high precision, and high resolution in the advanced FA lab that serves leading-edge semiconductor manufacturing.