Based on a computational model involving finite element method, we report the morphological evolution and pattern formation process in a thin polymer film subject to an externally imposed periodically varying heterogeneous DC electric field, induced by topographically patterned top electrode. Quasi-steady state morphology is observed to depend on remnant liquid layer after the evolution of primary structures. The dynamics of remnant layer de-wetting that essentially is dictated by electrode assembly, fluid properties, and initial film thickness, results in formation of intermediate secondary structures. The possibility of controlling these structures is explored by varying periodicity of the stamp/top electrode, applied potential and initial liquid volume. At a fixed operating condition, critical periodicity is identified for stable secondary structure formation that may lead to ordered nano-patterns for diverse applications.