The National Institute of Meteorological Research (NIMR) has operated the Fourier Transform InfraRed (FTIR) spectrometer which is the Atmospheric Emitted Radiance Interferometer (AERI) in Anmyeon island, Korea since June 2010. The ground-based AERI with similar hyper-spectral infrared sensor to satellite could be an alternative way to validate satellite-based remote sensing. In this regard, the NIMR has focused on the improvement of retrieval quality from the AERI, particularly clouddata filtering method. The AERI spectrum which is measured on a typical clear day is selected reference spectrum and we used region of atmospheric window. We performed test of threshold in order to select valid threshold. We retrieved methane using new method which is used reference spectrum, and the other method which is used KLAPS cloud cover information, each retrieved methane was compared with that of ground-based in-situ measurements. The quality of AERI methane retrievals of new method was significantly more improved than method of used KLAPS. In addition, the comparison of vertical total column of methane from AERI and GOSAT shows good result.