The continuing reduction in device dimensions and the adoption of complex three-dimensional (3D) designs pose significant challenges for process control. To characterize such 3D structures, Transmission Electron Microscopy (TEM) requires ultra-thin samples produced quickly and reliably. The CLM-3D DualBeamTM uses focused ion beam milling (FIB) and SEM imaging to analyze 3D structures as well as prepare samples for subsequent TEM analysis. Then FEI TEMLinkTM automates the transfer of these very small samples from the wafer to a TEM grid. This paper describes the integrated, efficient process produced by these tools.