Few techniques are available where the morphology of blends can be determined in all three dimensions on a nanometer scale. Here we describe the use of a combination of techniques to resolve the morphology both laterally and vertically in spin cast films of a poly(p-phenylene vinylene)/methanofullerene blend. These blends are used as photoactive films in plastic bulk heterojunction solar cells where the performance strongly depends on the molecular morphology. In addition to depth profiling by dynamic time-of-flight secondary ion mass spectrometry (TOF-SIMS), tapping-mode atomic force microscopy (TM-AFM), transmission electron microscopy (TEM), absorption and emission spectroscopy and time-correlated single photon counting fluorescence measurements were used to investigate the morphology of ~100 nm thick spin cast composites with varying composition of 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-methanofullerene (PCBM) and poly[2-methoxy-5-(3',7'-dimethyloctyloxy)-1,4-phenylene vinylene] (MDMO-PPV). Combining all results showed clustering of PCBM into rather pure separate domains in a matrix of ~50 wt% MDMO-PPV for composites with PCBM concentrations 80-100 wt%, and no spontaneous stratification. Electrical characterization, under illumination and in the dark, of the composite devices revealed the percolation threshold for electron transport and showed a reduction in recombination-limitation for the photocurrent of these solar cells as a result of an improved charge transport and collection efficiency with increasing fullerene concentration.