The cellulose microfibrils (CMF) from natural lignocellulosics are newly understood and exciting biomaterial constituent that can provide strong reinforcement in many products, including polymer composites. In this study, the cellulose crystals were extracted from jute and bagasse fibers based on the formic acid/ peroxyformic acid/peroxide process at atmospheric pressure, and their yields were 59.8 and 38.1%, respectively. Considering the biorefinery concept, the dissolved lignin and hemicelluloses in the processes were also isolated from the spent formic acid liquor. The results showed that the spent liquor contained 10.6 and 28.2% (on oven dried raw material) total sugars, and 10.9 and 16.9% lignin for jute and bagasse fibers, respectively. The xylose was the dominant sugar in the spent liquor. The cellulose microfibrils were further prepared from the extracted cellulose based on the acid hydrolysis technique. A very high yield of cellulose microfibrils (48.0 % based on the jute raw material) was obtained from jute fibers, while only 18.2% yield was obtained from the bagasse. The acid hydrolysate of jute cellulose contained 5.52% sugar, while bagasse hydrolysate contained 17.71% of sugars. The CMF samples obtained from the two different raw materials were characterized by means of TGA, FTIR, XRD, and TEM techniques. The average diameter of the CMF was 15-40 nm. The XRD results revealed that both CMF had a high crystallinity index. The thermal stability of MCC/NCC from the jute fibers was higher than that from the bagasse.