This paper presents a judicious reasoning method by coupling passive voltage contrast (PVC) with scanning probe microscopy (SPM) for revealing particular invisible defect modes, which were imperceptible to observe and very difficult to identify by means of traditional physical failure analysis techniques. In order to certify this compound method, it is applied to an implant issue as a case study. Through solving this particular defect mode, whose exact failure position could not be determined even with the most sensitive PVC or high-resolution SPM current mapping, the procedures and contentions are illustrated further. The significance of the reasoning method is based on electrical characterization and differential analysis. By coupling PVC with SPM, the capability to identify tiny defects is not limited to just distinguishing leakage or high-resistance under contacts. PVC can detect abnormal N+ contacts due to improper implanting, and SPM can provide the precise electrical characteristics.