This article demonstrates the value of atomic force microscopes, particularly the different electrical modes, for characterizing complex microelectronic structures. It presents experimental results obtained from deep trench isolation (DTI) structures using SCM and SSRM analysis with emphasis on the voltage applied by the AFM. From these measurements, a failure analysis workflow is proposed that facilitates AFM voltage optimization to reveal the structure of cross-sectioned samples, make comparisons, and determine the underlying cause of failures.