A method for detecting substrate damage in a flip chip die, having a back side and a circuit side, that uses magnetic resonance imaging. The back side of the die is first globally thinned down and a region for examination is selected. A magnetic field is applied to the selected region and then the region is scanned with a magnetic resonance imaging arrangement. A plurality of perturbations are measured to generate an array of perturbation signals, which are then converted to a local susceptibility map of the selected region of the die. The susceptibility map of the selected region is then examined to determine if there is any substrate damage.