We investigate the influence of annealing on the morphology of intimately mixed blends of the conjugatedpolymers poly(9,9′-dioctylfluorene-co-bis-N,N′-(4-butylphenyl)-bis-N,N′-phenyl-1,4-phenylene-diamine) (PFB) andpoly(9,9′-dioctylfluorene-co-benzothiadiazole) (F8BT) with scanning transmission x-ray microscopy(STXM). Through the use of a zone plate with theoretical Rayleigh resolution of 30 nm, weare able to resolve sub-100 nm bulk structure in these films. Surprisingly, for unannealedfilms spin-coated from chloroform we observe features with an average diameter of85 nm. The high degree of photoluminescence quenching in these as-spun films(>95%)implies that there is significant intermixing within the 85 nm structures, indicating that a hierarchyof phase separation exists even on the length scale of less than 100 nm. With annealing up to160 °C, closeto the Tg of the components, there is little change in the feature sizes observed by STXM, althoughan increase in variation of the composition is observed. With annealing above160 °C the imaged features begin to evolve in size, increasing to 225 nm inextent, alongside large changes in composition with annealing to200 °C. Comparing the evolution of morphology imaged by STXM with the change inphotoluminescence quenching with annealing, we propose that phase separationfirst evolves via the evolution of relatively pure phases on the length scale of afew to tens of nanometres within the larger 85 nm structures. Once the lengthscale of compositional fluctuations exceeds 85 nm (for anneal temperatures above160 °C) the hierarchy of phase separation is lost and the subsequent morphological evolution isreadily imaged by STXM. Applying the results of an exciton diffusion and quenchingmodel, we find good agreement between the size of the domains measured by STXM (above180 °C) and the results of the model for an exciton diffusion length of 15 nm. The growth indomain size and towards purer structures has also been observed with resonant soft x-rayscattering.