We combine Electro Optical Terahertz Pulse Reflectometry (EOTPR), with full three dimensional device-under-test (DUT) modeling utilizing virtual known good device to quickly and non-destructively isolate faults in advanced 3D IC packages. Computation power required for modeling can quickly become prohibitive with the design complexities of modern IC packages. In this study we adopt a piecemeal modeling approach that bypasses this exponential requirement. A PFA study verifies the accuracy of our model. This shows that feature-based fault analysis with a distance-to-defect accuracy of less than 10 μm can be readily attained through the combination of these techniques.