Embedded non-volatile memory (NVM) technologies are used in almost all areas of semiconductor chip applications, as it becomes increasingly vital to retain information when the electronics power is off. Nano-probing techniques, such as atomic force probe (AFP), allow us to access individual devices at contact or via levels and characterize the details as much as possible before a decision can be made for physical analysis. This paper reports the application of AFP to characterize each individual bit at contact level or individual column at via1 level. It presents two cases to identify the failures encountered in fabricated embedded NVM: column-column leakage and single bit erase failure. The first case shows that silicide residual could cause column to column leakage by creating electrical path between active areas of adjacent columns, while the second case shows that single bit failures due to low erase current can be recovered with repeated program/erase cycle.