We have demonstrated a visualization method of carbon nanotubes (CNTs) in water with fluorescent microscopy by using fluorescent dye background conditions that display a reversal contrast. We have successfully observed CNTs under a constant excitation light for more than ten minutes. We have developed novel chip system to supply fluorescence dye with appropriate concentration. The salt reaching method has been applied to PDMS (poly-dimethyl siloxane) in order to obtain porous structures. We have found that this porous structure provides homogeneous concentration of fluorescence dye by putting it in water and found out porous-PDMS support with larger porous gives a higher and steady concentration. The fine control of the concentration of the fluorescence dye in the microchannel has been achieved with a controlled speed of flow and mixture by means of a micro magnetic stirrer. Dielectrophoretic force was used for CNTs deposition onto electrodes that consist of transparent conductive film. It was confirmed that the proposed microfluidic system controls the concentration of fluorescent dye for a long term observation in water and is useful to apply CNTs to several biological application fields.