Abstract This paper covers methods used to isolate single leaky junctions in a test structure designed for Flash memory technology development. It may be possible to isolate this failure through micro probing or a combination of electrical testing and physical structure modification by FIB, but at the expense of spending numerous days. The paper shows that a combination of emission microscopy (EMMI), electron beam induced current (EBIC) characterization and a SEM nano-probing can drastically simplify the fault isolation process. Results of nano-probing are also shown to prove the level of leakage detected in the faulty junction. A combination of EMMI and EBIC characterization was able to pinpoint the problematic junction from approximately 2500 junctions in the structure. Furthermore, the nano-probing IV characterization proved the identified junction to be indeed high in leakage current, providing further confidence for physical failure analysis.