The film morphology of thin polymer blend films based on poly[(1-methoxy)-4-(2-ethylhexyloxy)-p-phenylenevinylene] (MEH-PPV) and poly(N-vinylcarbazole) (PVK) is probed as a function of film thickness. Blend films are prepared with spin-coating of polymer solutions with different concentrations on top of solid supports. The blending ratio of both conducting polymers is kept constant. The film and surface morphology is probed with grazing incidence ultrasmall-angle X-ray scattering (GIUSAXS) and atomic force microscopy (AFM). A linear dependence between the film thickness and the averaged phase separation is found. In addition, X-ray reflectivity measurements show an enrichment of PVK at the substrate interface. UV/vis spectroscopy measurements indicate a linearly increasing amount of both homopolymers in the blend films for increasing film thicknesses. The generalized knowledge about the influence of the film thickness on the phase separation behavior in conducting polymer blend films is finally used to describe the phase separation formation during the spin-coating process, and the results are discussed in the framework of an adapted Flory-Huggins theory for rodlike polymers.