With the evolution of advanced process technology, failure analysis has become more and more difficult because more defects are of the non-visual type (very tiny or even invisible defects) from new failure mechanisms. In this article, a novel and effective methodology which couples the conductive atomic force microscope (C-AFM) with nano-probing technique is proposed to reveal some particular failure modes which were not observable and difficult to identify with traditional physical failure analysis techniques. The capability of coupling C-AFM with nano-probing technique is used to distinguish cases which suffer general junction leakage or gate leakage from those that form the fake junction leakage or gate leakage cases. C-AFM can detect the abnormal contacts quickly, and nano-probing could provide the precise electrical characteristic further. Then, combining these variant measuring results, the favorable tactics can be adopted to deal with different states.