Advanced packages such as 2.5D will continue to grow in demand as performance increases are needed in various applications. Failure analysis must adapt to the changes in the interfaces, materials and structures being developed and now utilized. Traditional techniques and tools used for selectively removing materials to isolate and analyze defects need to evolve alongside these packages. A CF4-free Microwave Induced Plasma (MIP) process is used to remove underfill (UF) with minimal alteration of other materials on the samples, a process which has become more difficult on 2.5D modules. UF is removed using this MIP process to allow subsequent analysis on interposer interconnects and ìbumps in crosssection. SEM inspection, Electron Beam Absorbed Current (EBAC), and FIB are techniques used post cross-sectional UF removal of these 2.5D structures. The benefits of the specific MIP process through case studies are presented. Specifically, the use of an automatic cleaning step and a CF4-free downstream O2 plasma allow easy removal of UF without damaging other structures of interest with little tool recipe development.