The ability to control organic-organic interfaces in conjugated polymer blends is critical for further device improvement. Here, we control the phase separation in blends of poly (9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) and poly(9,9-di-n-octylfluorene-alt-(1,4-phenylene-((4-sec-butylphenyl)imino )-1,4-phenylene) (TFB) via chemical modification of the substrate by microcontact printing of octenyltrichlorosilane molecules. The lateral phase-separated structures in the blend film closely replicate the underlying micrometer-scale chemical pattern. We found nanometer-scale vertical segregation of the polymers within both lateral domains, with regions closer to the substrate being substantially pure phases of either polymer. Such phase separation has important implications for the performance of light-emitting diodes fabricated using these patterned blend films. In the absence of a continuous TFB wetting layer at the substrate interface, as typically formed in spin-coated blend films, charge carrier injection is confined in the well-defined TFB-rich domains. This confinement leads to high electroluminescence efficiency, whereas the overall reduction in the roughness of the patterned blend film results in slower decay of device efficiency at high voltages. In addition, the amount of surface out-coupling of light in the forward direction observed in these blend devices is found to be strongly correlated to the distribution of periodicity of the phase-separated structures in the active layer.