To recognize ground objects with infrared spectrum high frequency noise removing is one of the most important phases In spectrum feature analysis and extraction. A new method for infrared spectrum preprocessing was given combining spectrum continuum processing and Fast Fourier Transform (CFFT). Continuum Was firstly removed from the noise polluted infrared spectrum to standardize hyper spectra. Then the spectrum Was transformed into frequency domain (FD) with fast Fourier transform (FFT) separating noise information from target information. After noise eliminating from useful information with a low-pass filter, the filtered FD spectrum was transformed into time domain (TD) with fast Fourier inverse transform. Finally the continuum was recovered to the spectrum, and the filtered infrared spectrum was achieved. Experiment was performed for chlorite spectrum in USGS polluted with two kinds of simulated white noise to validate the filtering ability of CFFT by contrast with cubic function of five point (CFFP) in time domain and traditional FFT in frequency domain. A circle of CFFP has limited filtering effect so it should work much with more circles and consume more time to achieve better filtering result. As for conventional FFT, Gibbs phenomenon has great effect on preprocessing result at edge hands because of special character of rock or mineral spectra. while work., well at middle bands. Mean squared error of CFFT is 0. 000 012 336 with cut-off frequency of 150, while that of FFT and CFFP is 0. 000 06 1 074 with cut off frequency of 150 and 0. 000 022 963 with I-DO working circles respectively. Besides the filtering result of CFFT can be improved by adjusting the filter cut-off frequency, and has little effect on working time. The CFFT method overcomes the Gibbs problem of FFT in spectrum filtering, and can be more convenient, dependable, and effective than traditional TD filter methods.