Concentrated trifluoroacetic acid (TFA) is known to depolymerize cellulose. In this paper we report the effect of temperature and treatment time on physiochemical and morphological changes to cellulose. We present x-ray diffraction, SEM, degree of polymerization, and FTIR characterizations and compare them to acid-catalyzed hydrolysis of the decrystalized cellulose and conversion of the resultant glucose to HMF and levulinic acid by maleic acid-AlCl3 catalysis. Treatment with concentrated TFA for 2 hrs at 0°C resulted in a 28% reduction in crystallinity index (CrI) of the cellulose. Additional treatment for 5 hrs at 50°C resulted in a CrI of 0. Both changes of crystallinity index (CrI) resulted in about 40% improvement in overall yield of HMF and levulinic acid. Enzymatic hydrolysis study shows that TFA treatment for 2 hrs at 0°C results a 52% glucose conversion yield, which had higher conversion yield than the additional treatment for 5 hrs at 50°C with 45% glucose conversion yield. Results showed the additional reduction in CrI through heating step does not further improve yields from enzymatic hydrolysis.