Challenging multi-modal optimization problems have been very successfully solved by evolutionary computation (EC) techniques. To date, many methods have been proposed on evolutionary optimization for both single and multiobjective large scale problems. In the age of Big Data, there is an urge to take evolutionary optimization techniques to the next level for solving problems with even larger scales: thousands and millions of variables. These problems arise in many domains ranging from bioinformatics, to neuroscience and social simulations. In this paper, we investigate the use of EC to solve Big electroencephalography (EEG) data optimization problems with thousands of variables. The optimization problem attempts to identify maximum information that should be kept from a signal while minimizing the artifact. The high level of epistasis inherent in a signal can slow down the evolution. Therefore, we investigate the advantages of optimizing the problem in the frequency domain with different thresholds as opposed to the time domain. We propose synthetic EEG data sets of various scale and noise level. These data sets were the basis for the Optimization of Big Data 2015 Competition (BigOpt), CEC 2015. Two state-of-art multiobjective evolutionary algorithms (MOEAs) were evaluated. The results of this work suggest that frequency representation of the signals facilitates dimensionality reduction for big scale optimization of time series data, and hence provides faster and better quality solutions for EEG data cleaning. Moreover, the results suggest that existing state-of-art multiobjective evolutionary computation methods are extremely slow. Methods that can optimize the problem faster and with high quality are needed.