New heterogeneous 3D integration schemes and continuing miniaturization of semiconductor packaging components, such as micropillars, are driving demand for substantive changes to conventional PFA (physical failure analysis). In particular, desired performance capabilities include the ability to nondestructively determine failures within seconds to minutes. New tools should be quantitative, have sufficient resolution to determine sub-micron sized defects and voids in TSVs at the wafer or package level. It should also measure thickness and their material composition of multilayer structures above the wafer surface, such as microbumps, or those below the surface including UBM and RDL. In this paper we are introducing a novel x-ray fluorescence microscope technique capable of solving the above applications in advanced packaging for PFA and process development. The same technique can also be applied in the front end metrology of new gate materials, 3D FinFET structures within test structures in patterned wafers. Characterization of sub nanoscopic changes (sensitivity of sub-angstrom) in film and dopants deposited in 3D structures will also be shown. With its high sensitivity for trace materials, contamination analysis of post hard mask residue, post metal etch residue especially in high aspect ratio structures is also possible.