Refining is the major process of paper formation. This study focuses on the impact of a specific enzyme (Paenibacillus cellulase) for fibers on the surfaces, the roughness and height of the fibers are also investigated. Effects of enzyme dosages and the mechanical refining action (PFI revolution) on fiber physical properties were also analyzed. The fibers were observed by scanning electron microscopy (SEM), their roughness and height were analyzed by Atomic force microscopy (AFM). Results show that the Paenibacillus cellulase pretreatment increased the drainability of both kinds of pulp at the same level of refining energy. In other words, enzymatic treatment on pulp refining consumed less refining revolutions to reach the same drainability compared to the untreated pulp. Although the viscosity of both kinds of pulp was degraded with the enzymatic treatment, the physical properties of paper had no significantly negative influence on them. The results indicated the treatment with cellulase swelled the fibers in the absence of refining, and there were better fibrillation on the fibers treated with cellulase after refining. Furthermore, the statistical analysis of AFM suggested that both kinds of pulp treated with low cellulase dosage with PFI refining had higher roughness.