Carbon nanotubes (CNTs) have been successfully synthesized by using Double Stage Chemical Vapor Deposition (DS-CVD) technique, using acetylene (C2H2) and hydrogen (H2) as teh precursor gases. The morphology and the structure of CNTs were then characterized using Field Emission Scanning Electron Microscope (FESEM) , Transmission Electron Microscope (TEM) and Thermogravimetric Analysis (TGA). The effect of the process parameters were investigated whereby the experimental design of the investigation was conducted using Design Expert Version 6.0. The statistical analysis reveals that the optimized conditions for the best CNTs production is at 850C reaction temperature, 60 min reaction time, with gases flow rates at 40 and 150 ml/min for C2H2 and H2 respectively. CNTs produced were used as column chromatographic media. Due to its nano-sized structured dimension, CNTs has tremendously large surface area and that lead to highly efficient protein purification.