This paper discusses the Failure Analysis methodology used to characterize 3D bonded wafers during the different stages of optimization of the bonding process. A combination of different state-of-the-art techniques were employed to characterize the 3D patterned and unpatterned bonded wafers. These include Confocal Scanning Acoustic Microscopy (CSAM) to determine the existence of voids, Atomic Force Microscopy (AFM) to determine the roughness of the films on the wafers, and the Double Cantilever Beam Test to determine the interfacial strength. Focused Ion Beam (FIB) was used to determine the alignment offset in the patterns. The interface was characterized by Auger Spectroscopy and the precession electron nanobeam diffraction analysis to understand the Cu grain boundary formation.