The need to miniaturize in the electronics industry is driving smaller form factors, and resulting in complex packaging innovations such as structures with multiple devices stacked inside a three dimensional package. These structures present a challenge for non-destructive fault isolation. Two such modules recently exhibited failures on the NASA Goddard Space Flight Center Solar Dynamic Observatory (SDO) during board-level testing. Each module consisted of eight vertically-stacked mini-boards, each mini-board with a single EEPROM microcircuit and capacitor, and connected by external gold metallization to module pins. Both failed modules exhibited low-resistance shorts between multiple pins. The orthogonal structure of the module prompted the use of magnetic current imaging (MCI) in three planes in order to construct an internal three-dimensional current path for each of the failed modules. Magnetic current imaging is able to “look through” non-magnetic, or de-gaussed packaging materials, allowing global imaging without physical deprocessing of the stacked EEPROM modules, in order to construct the internal current path and localize defects. To our knowledge, this is the first time that this has been done. Following global isolation of the defects, two types of magnetic sensors were used in parallel with limited deprocessing in order to more precisely characterize suspect failure locations before actually physically exposing the defects. This paper will show the process for using magnetic current imaging with both SQUID and magnetoresistive (GMR) sensors to isolate defects in two stacked EEPROM packages along with the final physical analysis of the defects. The failure analysis found that these devices were damaged by external heat, possibly during oven pre-conditioning or hot air soldering onto the board. The manufacturer, 3-D Plus, was not implicated in the failure.