Spin-coated thin films of poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (APFO-3) blended with [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) are used as the active material in polymer photovoltaic cells. Such blends are known for their tendency to phase separate during film formation. Tuning the morphology of the blend in a controlled way is one possible road towards higher efficiency. We studied the effect of adding chlorobenzene to chloroform-based blend solutions before spin-coating on the conversion efficiency of APFO-3:PCBM photodiodes, and related that to the lateral and vertical morphology of thin films of the blend. The lateral morphology is imaged by atomic force microscopy (AFM) and the vertical compositional profile is obtained by dynamic secondary ion mass spectrometry (SIMS). The profiles reveal compositional variations consisting of multilayers of alternating polymer-rich and PCBM-rich domains in the blend film spin-coated from chloroform. The vertical compositional variations are caused by surface-directed spinodal waves and are frozen in during the rapid evaporation of a highly volatile solvent. With addition of the low-vapour pressure solvent chlorobenzene, a more homogeneous vertical composition is found. The conversion efficiency for solar cells of this blend was found to be optimal for chloroform:chlorobenzene mixtures with a volume-ratio of 80:1. We have also investigated the role of the substrate on the morphology. We found that blend films spin-coated from chloroform solutions on PEDOT:PSS-coated ITO show a similar compositional structure as the films on silicon, and that changing the substrate from silicon to gold only affects the vertical phase separation in a region close to the substrate interface.