The objective of the present work was to evaluate the use of Raman microspectroscopy analysis to assess changes in cellulose micro/nanofibril structure from fibers subjected to different pre-treatments. Pulp fibers were pre-treated with 5 wt% NaOH for 2 h, 10 wt% NaOH for 1 h, and endoglucanase-type enzymes to improve nanofibrilation. After the pre-treatments, the fibers were mechanically fibrillated to produce cellulose micro/nanofibrils, which were made into films to be analyzed. Fibers pre-treated with 5 wt% NaOH produced 59% micro/nanofibrils with average diameter less than 30 nm, for Eucalyptus, and 46% of micro/nanofibrils, with the same diameter, for Pinus. However, the enzymatic pre-treatment was the most efficient, resulting in 83% of micro/nanofibrils for Eucalyptus and 78% for Pinus. This corroborates with the lowest values of the 1.096/2.896 ratio and degree of polymerization, indicating chain shortening in cellulose. X-ray diffraction and Raman microspectroscopy crystallinity results presented similar tendencies, with increased crystallinity caused by all pre-treatments, being 5 wt% NaOH for 2 h the highest, with 70%, for Eucalyptus and Pinus. Enzymatic pre-treatment has produced the best fibrillation and greater crystallinity. The present work has shown a reliable way of assessing cellulose structure using Raman microspectroscopy.