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This paper proposes a windowing frequency domain adaptive filter and an upsampling block transform preprocessing to solve the stereo acoustic echo cancellation problem. The proposed adaptive filter uses windowing functions with smooth cutoff property to reduce the spectral leakage during filter updating, so the utilization of the independent noise introduced by preprocessing in stereo acoustic echo cancellation can be increased. The proposed preprocessing is operated in short blocks with low processing delay, and it uses frequency-domain upsampling to meet the minimal block length requirement given by the band limit of simultaneous masking. Therefore, the simultaneous masking can be well utilized to improve the audio quality. The acoustic echo cancellation simulations and the audio quality evaluation show that, the proposed windowing frequency domain adaptive filter performs better than the conventional frequency domain adaptive filter in both mono and stereo cases, and the upsampling block transform preprocessing provides better audio quality and stereo acoustic echo cancellation performance than the half-wave preprocessing at the same noise level.