The morphological evolution of laterally phase-separated polyfluorene blends composed of poly(9,9′-dioctylfluorene-co-bis-N,N′-(4-butylphenyl)-bis-N,N′-phenyl-1,4-phenylenediamine) (PFB) and poly(9,9′-dioctylfluoreneco-benzothiadiazole) (F8BT) has been studied with scanning transmission X-ray microscopy (STXM). The degree of phase separation in the films was regulated by controlling the time spent in a solvent-saturated atmosphere during solution processing, typically between 1 and 6 min. For films with a 5:1 weight ratio of PFB:F8BT, we observe a systematic increase in domain size and domain purity, with the enclosed F8BT-rich domains growing both through coalescence and flow of material across the domain boundary. For 1:1 and 1:5 blends a more complicated evolution of morphology is observed with evidence of additional vertical stratification. For 1:1 blends, primary and secondary phase separation is observed, with the evolution of the PFB-rich phase evolving similar to the 5:1 blend. Interestingly,the PFB-rich spots within the F8BT domain are observed to disappear after around 3 min of morphology evolution. Similar behavior is also seen in 1:5 blends, where a dramatic partial phase inversion is observed. The origin of this transition is attributed to subsequent vertical phase separation, with PFB wetting the substrate/film interface or film/vapor interface or both. In addition to the mechanisms of phase separation, the implications of the observed morphology changes for device performance are also discussed.