Imaging critical features by using transmission electron microscopy (TEM) or scanning electron microscopy (SEM) provides a versatile approach for nanostructure characterization. The combination of focused ion beam (FIB) technology for exposing defective sites beneath the surface is shown. Reliability testing and defect analysis by localized characterization of multilayered structures is demonstrated. TEM-imaging of a transistor gate with a locally confined radiation damage demonstrates target preparation by FIB yielding high-resolution TEM samples. The TEM imaging requires a longer sample preparation but provides high image quality (TEM). Investigation of materials previously processed with FIB revealed amorphization damage by the high energetic Ga-ion beam. This damage layer with a thickness in the range of 50 to 100 nm was confirmed in simulation. This disadvantageous damage by amorphization originating from FIB preparation of the cross-section could be removed by soft sputtering with a 250 V Ar+ ion beam. This combined method using FIB for microsample preparation and TEM for imaging and analysis was proven to be a powerful tool the exploitation of nanostructured devices and for defect analysis on a highly localized scale.