A scanning spectral filter method to improve the signal-noise-ratio in the femtosecond chains is proposed by using the characteristic that the instantaneous frequency varies with the time approximately linearly for the chirped pulse in the time-frequency domain. The scanning spectral filtering for reduing the amplification of spontaneous emission (ASE) intensity is analyzed in the time-frequency domain by using the Short-Time Fourier Transform method. The results show that the pulse contrast can be improved by two orders, and the transmission efficiency of the chirped pulse can exceed 90% when the synchronizing time jitter ranges from -2ps to 2ps and the chirp rate p from 0.9C/T2 to 1.10C/T2. Adopting the cascaded scanning filter to improve the pulse contrast is investigated too, which can improve the pulse contrast effectively. The great advantage of this novel nonlinear spectral filter technology is high energy and high peak intensity femtosecond chains for it filters out the ASE in the near field in temporal domain.