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Filter bank multiple access (FBMA) without subbands orthogonality has been proposed as a new candidate waveform to better meet the requirements of future wireless communication systems and scenarios. It has the ability to process directly the complex symbols without any fancy preprocessing. Along with the usage of cyclic prefix (CP) and wide-banded subband design, CP-FBMA can further improve the peak-to-average power ratio and bit error rate performance while reducing the length of filters. However, the potential gain of removing the orthogonality constraint on the subband filters in the system has not been fully exploited from the perspective of waveform design, which inspires us to optimize the subband filters for CP-FBMA system to maximizing the achievable rate. Besides, we propose a joint optimization algorithm to optimize both the waveform and the covariance matrices iteratively. Furthermore, the joint optimization algorithm can meet the requirements of filter design in practical applications in which the available spectrum consists of several isolated bandwidth parts. Both general framework and detailed derivation of the algorithms are presented. Simulation results show that the algorithms converge after only a few iterations and can improve the sum rate dramatically while reducing the transmission delay of information symbols.