Interferogram filtering is a key technique in the process of spectral recovery of imaging Fourier transform spectrometer. Differential filtering and polynomial filtering are usually used, but differential filtering cannot filter the noise completely, and polynomial filtering, which needs the noise type when filtering, produces big bias at both ends of the interferograms. Empirical mode decomposition (EMD), a new signal processing method in linearity and stationary spectral analysis, is now widely used in many aspects. EMD technique is applied to interferogram filtering. It can avoid the disadvantages of differential filtering and polynomial filtering, and it is more reasonable to extract the background noise. The data acquired in the laboratory are used to analyze the precision of different filtering methods. The result indicates that the precisions of differential filtering, polynomial filtering and EMD are 0.0079, 0.0073, 0.0068, respectively. EMD is the optimum filtering method, followed by the polynomial filtering and differential filtering.