Brain electrical activity recorded via electroencephalogram (EEG) is the most convenient means for brain-computer interface (BCI), and is notoriously noisy. The information of interest is located in well defined frequency bands, and a number of standard frequency estimation algorithms have been used for feature extraction. To deal with data nonstationarity, low signal-to-noise ratio, and closely spaced frequency bands of interest, we investigate the effectiveness of recently introduced multivariate extensions of empirical mode decomposition (MEMD) in motor imagery BCI. We show that direct multichannel processing via MEMD allows for enhanced localization of the frequency information in EEG, and, in particular, its noise-assisted mode of operation (NA-MEMD) provides a highly localized time-frequency representation. Comparative analysis with other state of the art methods on both synthetic benchmark examples and a well established BCI motor imagery dataset support the analysis.