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An iterative method for the design of the non-uniform filter banks (NUFB) proposed by Soni et al is examined and improved by designing the prototype filters using the modified window such as Kaiser, Cosh and Exponential. These windows are modified by adding third parameter (ρ) which improves the spectral characteristic of the window in terms of smaller ripple ratio (RR), the wider main lobe width with improved side lobe roll-off ratio (SR). In this method, the cut-off frequency is varied iteratively in order to adjust the filter coefficients so that the reconstruction error is optimized to zero. Several design examples are included to demonstrate the efficacy of the modified window functions. A comparative study of performance of the different modified windows for designing non-uniform filter bank is made in terms of the reconstruction error, computational (CPU) time, and number of iteration (NOI). Finally, the modified windows are exploited for sub-band coding of electrocardiogram (ECG) signals.