Mixtures of conjugated polymers and quantum dot nanocrystals present an interesting solution-processable materials system for active layers in optoelectronic devices, including solar cells. We use scanning transmission electron microscopy to investigate the effects of exchanging the capping ligand of quantum dots on the three-dimensional morphology of the film. We created 3D reconstructions for blends of poly((4,8-bis(octyloxy)benzo(1,2-b:4,5-b’)-dithiophene-2,6-diyl)(2-((dodecyloxy)carbonyl)thieno (3,4-b)-thiophenediyl)) (PTB1) and PbS quantum dots capped with oleic acid (OA), butylamine (BA), OA to 3-mercaptopropionic acid (MPA), and BA to MPA. We use these reconstructed volumes to evaluate differences in exciton dissociation and charge transport as a function of ligand processing. We show that the MPA exchange without an intermediate BA treatment results in severe changes to the film structure and a non-ideal morphology for an effective device. We also show that with a BA exchange, the morphology remains largely unchanged with the additional MPA treatment. This quantitative characterization elucidates previously reported device performance changes caused by ligand exchange and should inform future device fabrication protocols.