The magnetic microstructure responsible for the metastable high resistance state of weakly coupled, as-prepared [Co(6 nm)/Cu(6 nm)]20 multilayers was analyzed using polarized neutron reflectivity and scanning electron microscopy with polarization analysis (SEMPA). This article focuses and expands on the SEMPA measurements. In multilayer structures such as these, SEMPA can be combined with ion milling to directly image the layer-by-layer magnetization and quantitatively depth profile the interlayer magnetic domain correlations. We found that in the as-prepared Co/Cu multilayer, the domains are about 1 μm in size and the magnetizations in adjacent layers are almost completely oppositely aligned. The relative magnetoresistance derived from this measured degree of anticorrelation is in agreement with the measured magnetoresistance.