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This paper presents a study of electrokinetic transport in a nano-fluidic chip that allow for separation and pre-concentration of the molecular mixtures into a high density multi-wall carbon nano tubes (MWCNTs) array of nano-channels. The MWCNTs array was used as an induced-surface charge filter to attract the opposite charged molecules on the wall surface by van der Waals and electrostatic force. The surface charge of MWCNTs is inversely proportional to the channel wall thickness and proportional the dielectric constant of itself and the applied external electric-field. A modified RuOx particles MWCNTs electrode was used as electrochemical sensor to increase the reactive surface area and reduce the redox potential for 0.1 muM insulin detection. 0.5 muM FITC (fluorescein) and Rhodamine 6G dye mixtures during the electrokinetic trapping process, could be easily to separate by the electric property of dyes in a MCNTs filter nanochannel, the concentration capability of FITC as high as 5000-10000 folds have been demonstrated. For electrochemical behavior, the RuOx/MWCNTs electrodes could be efficient to reduce about 0.055-0.06V oxide potential compared with MWCNTs only electrodes.