— This paper investigates both transmultiplexer (TMUX) and analysis-synthesis filter banks where the two sides of the filter bank system are of different sizes. Such configurations find applications in filter bank based multicarrier communication systems on one hand and in fractionally-spaced frequency domain equalizers on the other. The errors due to mismatched filter banks are analyzed. Based on this analysis, it is shown how to modify the subband processing to compensate the reconstruction error in the analysis-synthesis configuration, or the inter-carrier and inter-symbol interferences in the multicarrier case. The needed subband processing can be incorporated to the subband-wise channel equalizers with no additional complexity during data processing and minor additional complexity in the equalizer coefficient calculation and their adaptation.