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We present a new filter scheme for magnetocardiogram (MCG) signal processing based on the quasi-periodic characteristic of the signals. The key points of this scheme are to determine the exact numbers of data points in each cardiac cycle by using electrocardiogram (ECG) data acquired simultaneously with the MCG signal and to normalize the MCG data sequence in each cycle into an identical length. Compared with conventional filters, the scheme has the advantage of more powerful noise suppression with less signal distortion. The desire for having high quality output signals from raw MCG data acquired in a simple shielded room or even in unshielded environment may be realized with the scheme.