Abstract Damage-free gate oxide is one of the important factors to ensure device performance and reliability. Special wafer accepts test structures such as a large size MOS capacitor must be laid on test line to monitor the oxide process issue and process window. However, it brings about many challenges to failure analysis engineer. To overcome the EFA and PFA limitations, fresh samples were taken from the passed wafer and the failed ones to identify the root cause of VBD failure. A novel lapping down method was used to access the capacitor structure. Two VBD failure cases were studied. In this study, poor wet clean process was defined as the cause of the silicon substrate surface damage and crystalline defect. It induced poor oxide deposition, which reduced breakdown voltage. Additionally, 12hrs BOE dip was shown to be an effective method for removing poly and oxide layers from large MOS capacitors.