The precise extraction and purification of cell free DNA (cfDNA) is crucial for molecular diagnosis and treatment of personalized medicine in the cancer management. At present, spin column-based method for cfDNA extraction using centrifuge is most commonly used. However, there are several limitations, such as cross contamination and inconsistent efficiency, in conventional spin column method. Therefore, we developed vacuum pressure based automation system of cfDNA extraction to unify entire process under single driving mechanism. Extracted cfDNA from plasma was quantified by quantitative PCR (qPCR). The data of qPCR analysis was compared to the conventional method from QIAGEN. As a result, sufficiently equal efficiency of cfDNA extraction in the present system to the conventional method was obtained. In conclusion, our research would lead to the development of a fully automated system by integrating the entire process and manufacturing into a lab-on-a-chip device based micro fluidic.