Diesel engines are high thermal efficiency because of high compression ratio but produce high concentration of particulate matter (PM) because of direct injection fuel diffusion combustion. PM must be removed from the exhaust gas to protect human health. This research describes biodiesel engine performance, efficiency and combustion behavior using combustion pressure analyzer. It was clearly observed that PM emitted from CI engines can be reduced by using renewable bio-oxygenated fuels. The morphology and nanostructure of fossil fuel and biofuel PMs were investigated by using a Scanning electron microscopy (SEM) and Transmission electron microscopy (TEM). The morphology of biodiesel and diesel doesn’t have much different in the viewpoint of particulate matter trapping using DPF micro surface pores. The agglomerated ultrafine particles and primary nanoparticles sizes of diesel and biodiesel engine’s PM are approximately 50-500 nm and 20-50 nm, respectively. The primary particle of biodiesel engine’s PM is smaller than that of fossil diesel. The average of diesel and biodiesel PM’s carbon platelets is in the range of 0.2-5.2 nm.