In this research, we studied the morphological transformation of a poly(4-vinylpyridine), P4VP, thin film on a polyimide substrate after thermal nanoimprint and investigated its effect on electron beam (EB) exposure by atomic force microscopy. On the basis of the results, we designed a patterned double-layer thin film consisting of polystyrene, PSt, as the outermost inactive layer and P4VP as the underlying active layer for Cu electroless deposition. We studied how to prepare and confirm the integrity of a double-layer structure on the polyimide substrate after thermal nanoimprint. A P4VP thin film of 60 nm thickness started to be transformed by thermal nanoimprint at 80 °C owing to a thin-film effect lowering the glass transition temperature (Tg = 137°C) of its bulk state. EB exposure caused P4VP crosslinking and resulted in the P4VP layer becoming insoluble in toluene and being hardly transformed by thermal nanoimprint even at 160 °C. As a result, an outermost layer of PSt exhibiting a lower Tg than P4VP was successfully prepared by spin coating and was transformed only by thermal nanoimprint. The designed internal structure of the double-layer thin film patterned by thermal nanoimprint was confirmed by transmission electron microscopy (TEM) as a cross-sectional image using HAuCl4 and RuO4 as stain reagents for P4VP and PSt, respectively.