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Electroencephalograph (EEG) recordings during right and left hand motor imagery can be used to move a cursor to a target on a computer screen (such system is called BCI). Recently, we have proposed the detection method of error potential in order to add the fail safe function to BCI system. In this paper, feature extraction method based on morphological multi-resolution analysis is introduced to extract features concerned with motor imagery and cognition simultaneously from the EEG signals. Morphological filter is composed of nonlinear operation between signal and structural function and this multi-resolution analysis can be constructed by repeating this filtering to signal while changing structural function. This method is a kind of discrete wavelet analysis with non-linear characteristics and is effective to extract specific shapes. The structural function which decides the filter characteristic is designed to obtain optimal separation based on mutual information algorithm or spectrum dividing algorithm.