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In this letter, we report an energetics-based model to explain the self-organizing nanomesa and nanowell patterns recently observed in Langmuir-Blodgett (LB) films of polyvinylidene fluoride trifluoroethylene [P(VDF-TrFE)] copolymers. The feature size of nanomesas and nanowells has been estimated using a linear stability analysis, and the morphology of the nanomesas and nanowells has been revealed by the numerical simulation, both in good agreement with experiments. A number of other model predictions regarding the nanomesa and nanowell formation also agree with experimental observations. The model can be used to guide the design and optimization of nanostructures in the P(VDF-TrFE) LB films and possibly in other thin polymer films.