Material properties in polymer and fullerene bulk heterojunctions (BHJs) such as donor to acceptor volume fraction, morphology, and molecular orientation critically influence light absorption, exciton dissociation, charge transport, and recombination, all of which are crucial device properties in organic photovoltaics (OPV). Spatial variation of BHJ properties normal to the substrate, caused by phase segregation, can thereby create corresponding spatial variations in the OPVs optoelectronic properties. Here, normally incident and wave-guided optical modes are used to selectively excite localized regions within an inverted poly(3-hexythiophene-2,5-diyl) and phenyl-C61-butyric acid methyl ester BHJ OPV and corresponding internal quantum efficiencies are measured to study the spatial-dependent charge carrier collection probability within the BHJ. An electron-limited charge collection profile is observed for a thick (920 nm) BHJ due to fullerene-poor regions as a result of phase segregation. As the thickness of the BHJ is reduced (100 nm), charge transport is seen to be unaffected by the phase segregation. This has the potential to be a versatile non-destructive characterization technique for measuring the spatially varying charge collection probability in thin film photovoltaics and will help enable optimum device design and characterization.