This paper discussed on how the importance of failure analysis to identify the root cause and mechanism that resulted in the MEMS failure. The defect seen was either directly on the MEMS caps or the CMOS integrated chip in wafer fabrication. Two case studies were highlighted in the discussion to demonstrate how the FA procedures that the analysts had adopted in order to narrow down to the defect site successfully on MEMS cap as well as on CMOS chip on MEMS package units. Besides the use of electrical fault isolation tool/technique such as TIVA for defect localization, a new physical deprocessing approach based on the cutting method was performed on the MEMS package unit in order to separate the MEMS from the Si Cap. This approach would definitely help to prevent the introduction of particles and artifacts during the PFA that could mislead the FA analyst into wrong data interpretation. Other FA tool such as SEM inspection to observe the physical defect and Auger analysis to identify the elements in the defect during the course of analysis were also documented in this paper.