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In conductive electromagnetic interference (EMI) noise measurement, noise separation is important for noise diagnosis and suppression. Compared with conventional hardware-based separation, the noise soft separation, which is based on modern signal processing technique, is more robust, convenient and cheap. However, the non-ideal spectrum performance of current probes may have effects on the separation results. Thus in this paper, a compensation method is proposed for current probes applied in noise soft separation. Results show that the method is efficient in use.