This paper describes a novel technique for studying structure-transport correlations in nanoscale multilayer thin films. Here, local current-voltage characteristics from simplified magnetic tunnel junctions are measured in situ on cross-sectional transmission electron microscopy (TEM) samples and correlated directly with TEM images of the microstructure at the tunneling site. It is found that local variations in barrier properties can be detected by a point probe method, and that the tunneling barrier height and width can be extracted.