The available fuel sources in the market are less than demand, therefore the alternative fuels are substitutes for different commercial and residential applications, such as diesel and petrol for automobiles. Currently, many countries need to import significant amount of crude oil and other petroleum products. Also the air pollution is another environmental problem caused by the pollutant emissions from the automobiles running on petroleum products. The biogas is a renewable clean fuel that can potentially replace the traditional petroleum fuels in the future. Biogas contains 55% CH4, 40.5% Co2, and 4.5% pollutants including H2, N2, H2S, and O2 to minimize the pollutant amount. Biogas can be processed by going through the enrichment system of scrubbing and bottling mechanisms to produce Bio-CNG gas for automobiles. Biogas can be widely utilized after performing purification process to remove pollutants. The pure Bio- Methane in this analysis is pressurized to 19.5 MPa to fill in CNG cylinder by compressor. The capacity of producing Biogas is about 148 m3 daily and Biogas production efficiency will rely on environment and other conditions. The design analysis of bio-reactor in this biomass system is accomplished by performing the mathematical modeling, computer aided simulation, and prototype experiment.