We have studied the thin film morphology of a semiconducting polymer photovoltaic blend comprising an electron acceptor poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) and the donor poly(9,9′-dioctylfluorene-co-bis-N,N′-(4-butylphenyl)-bis-N,N′-phenyl-1,4 phenylenediamine) (PFB). The molecular weight and blend weight ratio of the constituent polymers were used to modify the morphology. The average chemical composition of the bulk of F8BT:PFB blend in thin films was mapped using Raman microscopy at different depths from the air-film interface through controlled successive etching from the upper surface layer using an oxygen plasma. Correlating the lateral to the vertical Raman analysis of the phase separation of the film (blend weight ratio of 50:50) reveals that the μm scale de-mixed lateral phase structure seen on the free surface is present throughout most of the film thickness, though there is also some F8BT content within the PFB-rich wetting layer on the glass substrate, which we consider is due to the F8BT-rich interface at the surface to the substrate. The dependence of photovoltaic performance on morphology is discussed.