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Achieving an efficient and reliable method is essential to interpret a user's brain wave and deliver an accurate response in biomedical signal processing. However, EEG patterns exhibit high variability across time and uncertainty due to noise and it is a significant problem to be addressed in mental task as motor imagery. Therefore, fuzzy components may help to enable a higher tolerance to noisy conditions. With the advent of Deep Learning and its considerable contributions to Artificial intelligence and data analysis, numerous efforts have been made to evaluate and analyze brain signals. In this study, to make use of neural activity phenomena, the feature extraction preprocessing is applied based on Multi-scale filter bank CSP. In the following, the hybrid series architecture named EEG-CLFCNet is proposed which extract the frequency and spatial features by Compact-CNN and the temporal features by the LSTM network. However, the classification results are evaluated by merging the fully connected network and fuzzy neural block. Here, the proposed method is further validated by the BCI competition IV-2a dataset and compare with two hyperparameter tuning methods, Coordinate-descent and Bayesian optimization algorithm. The proposed architecture that used fuzzy neural block and Bayesian optimization as tuning approach, results in better classification accuracy compared with the state-of-the-art literatures. As results shown, the remarkable performance of the proposed model, EEG-CLFCNet, and the general integration of fuzzy units to other classifiers would pave the way for enhanced MI-based BCI systems. [ABSTRACT FROM AUTHOR]