Multi-orientated bi-layered nano wire polarizers were fabricated in a polycarbonate (PC)substrate to eliminate the alignment error caused by the discrete components. The polarizers were used in a polarization navigation sensor, the angular error was tested and the angular error compensation algorithm based on neural network was analyzed. First, the bi-layered nano wire polarizers were designed using Rigorous Coupled Wave Analysis (RCWA) and the effects of grating period and metal layer thickness on the polarizer performance were analyzed in detail. Experiments show that the polarizer has TM transmittance of 71% and extinction ratio of 2 100 for the wavelength of 518 nm. The polarizer was fabricated based on nanoimprint lithography and six polarizers were mounted in the substrate with the same structure but different orientations. After that, the polarizer was applied to a polarization navigation sensor and the angular error was measured at a measurement platform. Results indicates that the original angular error is within ±1° , but it is ±0.2° when is compensated by using Back Propagation(BP) neural network compensation algorithm. The proposed polarizer could fulfill the needs of polarization navigation systems.