The interdigitated design for donor-acceptor in solar cell has been studied in some detail, but the optimum size and shape leading to direct enhancement in nanopore (or nanopillar) structure is still not well understood. Here, we demonstrate a modeling method to forecast the optimum size and shape for poly(3-hexylthiophene) (P3HT) nanopores in interdigitated P3HT: [6, 6]-phenyl C61 butyric acid methyl ester (PCBM) photovoltaic device, based on experimental results of P3HT:PCBM bilayer solar cell. In our analysis, the energy generated at unit nanopore is supposed to the same as the one generated at infinite point of P3HT:PCBM bilayer solar cell with variable layer thickness. A definitive function in terms of a radius of unit nanopore with various shapes is established, substituting a regression function derived from the results of power conversion efficiency in bilayer solar cell. Interpreting the function, we finally showed that the effective radius for P3HT nanopores with rectangular or cylinder, cut-cone, cone shape should be less than 135, 53, 2 nm respectively.