The three-dimensional morphology of mixed organic layers are quantitatively measured using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) with electron tomography for the first time. The mixed organic layers used for organic photovoltaic applications have not been previously imaged using STEM tomography as there is insufficient contrast between donor and acceptor components. Contrast is generated by substituting fullerenes with endohedral fullerenes that contain a Lu3N cluster within the fullerene cage. The high contrast and signal-to-noise ratio, in combination with use of the discrete algebraic reconstruction technique (DART), allows generation of the most detailed and accurate three-dimensional map of BHJ morphology to date. From the STEM-tomography reconstructions it is determined that three distinct material phases are present within the BHJs. By observing changes to morphology and mixing ratio during thermal and solvent annealing, the effects of mutual solubility and fullerene crystallization on morphology and long term stability are determined. This material/technique combination shows itself as a powerful tool for examining morphology in detail and allows for observation of nanoscopic changes in local concentration.