So far, most of the defects at system level are assembly related. This trend obviously concerns Systems in Package, Stacked dies, Packages on Package devices, passive integration, integration of logic, power, wireless, analog, sensor and actuator in the same packaged device… All these Systems in Package defy our failure localization tools. For the first time, we have to face non transparent material, massive 3D structure with mandatory long working distance and need of relatively high spatial resolution. Magnetic microscopy has the ability do this as long as we are able to adapt its principle to the mandatory 3D sensitivity and resolution. We have developed a global 3D approach based on simulation in order to target µm resolution at long working distance.