In this paper, we discuss a set of techniques and analysis methodologies for the reverse engineering and functionality extraction of complex mixed-signal ICs with a special focus for security applications. Front and back side reflected light pattern images at different magnifications are used to identify circuit blocks. Time-integrated and time-resolved photon emission data is used to identify gate logic states, sequences of events, and specific functional activity. Backscattered electron and scanning transmission electron images mosaics are used to reverse engineer individual gates and observe local interconnects. Thermal imaging is used to aid in the functional block identification and analog gates analysis. Different advanced methodologies for tool automation, focusing, mapping, and image processing are also discussed in the context of our proposed electro-optical tester based technique.