When it comes to complex system-in-package (SiP) with a wide spectrum of materials and packaging structures integrated into a single module, decapsulation and the following failure analysis become extremely complex. Previous work published by the authors' group has demonstrated that a halogen-free microwave induced plasma (MIP) system has great advantage compared to the conventional techniques mentioned before. This paper explores the applicability of the halogen-free MIP on the most complex SiP module decapsulation. Applications in special structures in SiP include 3D stacked-die, gallium arsenide, surface acoustic wave (SAW) and bulk acoustic wave filters, and copper re-distribution layer. The halogen-free MIP decapsulation process can expose and preserve all the dies and passive components as well as the original failure sites, which proves to be key to ensuring a high success rate in SiP failure analysis.