The 3D package configuration presents challenges to conventional Fault Isolation (FI) and Failure Analysis (FA) methods. This paper illustrates that with correct Electro Optical Terahertz Pulse Reflectometry (EOTPR) data processing, interpretation and additional reference spectra, the combination of EOTPR to isolate the open/high resistance failure location and 3D X-ray Computed Tomography (CT) to image the failure is very effective for System in a Package (SIP) FI/FA.