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As the feature size of FPGA shrinks to nanometers, SRAM-based FPGAs are more vulnerable to soft errors. During logic synthesis, reliability of the design can be improved by introducing logic masking effect. In this work, we observe that there are a lot of not-fully occupied look-up tables (LUTs) after logic synthesis. Hence, we propose a functional equivalent class based soft error mitigation scheme to exploit free LUT entries in the circuit. The proposed technique replaces not fully-occupied LUTs with corresponding functional equivalent classes, which can improve the reliability while preserve the functionality of the design. Experimental results show that, compared with the baseline ABC mapper, the proposed technique can reduce the soft error rate by 21%, and the critical-path delay increase is only 4.25%.