Solution processable fullerene and copolymer bulk heterojunctions are widely used as the active layers of solar cells. In this work, scanning time-of-flight secondary ion mass spectrometry (ToF-SIMS) is used to examine the distribution of [6,6]phenyl-C61-butyric acid methyl ester (PCBM) and regio-regular poly(3-hexylthiophene) (rrP3HT) that forms the bulk heterojunction. The planar phase separation of P3HT:PCBM is observed by ToF-SIMS imaging. The depth profile of the fragment distribution that reflects the molecular distribution is achieved by low energy Cs(+) ion sputtering. The depth profile clearly shows a vertical phase separation of P3HT:PCBM before annealing, and hence, the inverted device architecture is beneficial. After annealing, the phase segregation is suppressed, and the device efficiency is dramatically enhanced with a normal device structure. The 3D image is obtained by stacking the 2D ToF-SIMS images acquired at different sputtering times, and 50 nm features are clearly differentiated. The whole imaging process requires less than 2 h, making it both rapid and versatile.