The surface EMG signal detected from voluntarily activated muscles can be used as a control signal for functional electrical stimulation. To use the voluntary EMG signal, it is necessary to eliminate the muscle response evoked by the electrical stimulation and enable to process the algorithm in real time. In this paper, we propose the Gram-Schmidt(GS) algorithm and implement it in FPGA(field programmable gate array). GS algorithm is efficient to eliminate periodic signals like muscle response, and is more stable and suitable to FPGA implementations than the conventional least-square approach, due to the systolic array structure.