Nanoimprint lithography is applied to fabricate topographically uniform patterns onto demixed polymer blend films. The high fidelity of pattern replications is achieved for 150 nm polystyrene (PS)/polymethylmethacrylate (PMMA) blend films with varying compositions. When imprinted at 150 °C, the morphology of the blend across the patterned structures is similar to that in the as-casted films. Significant morphological evolutions occur for patterns imprinted at 180 and 210 °C. For all the patterns, PMMA is found to segregate into the residual layer, driven by the preferential wetting of PMMA onto the SiO(x) surfaces. The combined domain coarsening and preferential wetting of PMMA leads to the formations of unique encapsulated structures within the topographically uniform features, ranging from blocks to threads.