To compare flap adhesion strength, stromal bed quality, and tissue responses after flap preparation using nJ- and μJ-energy level femtosecond lasers. All corneal flaps were created by either VisuMax laser (μJ-energy level) or femto-LDV (nJ-energy level). Flap adhesion strength in the rabbits was measured with a tension meter 1 and 2 months postoperatively. To investigate tissue responses to laser delivery, immunofluorescence staining and TUNEL assay were performed 4 and 24 hours postoperatively. To assess flap bed smoothness, human donor corneas were used. Surface irregularities were graded based on scanning electron microscopy results. The flap adhesion strength in the VisuMax group at month 1 and 2 was 16.95 ± 1.45 kPa and 18.33 ± 1.81 kPa, respectively; and 12.31 ± 4.15 kPa and 13.85 ± 4.78 kPa in the LDV group, respectively. No significant difference was found between the groups. Fibronectin and apoptotic cells were largely absent at the central incision site in the LDV group, but were present in the VisuMax group. The smoothness of flap beds appeared similar for both groups. An observer scored the VisuMax group 8.00 ± 1.00 and the LDV group 7.33 ± 0.58 (P = 0.387). The flap adhesion strength increased over time after treatment with both lasers. The nJ-energy pulses produced minimal wound healing reaction and apoptotic cells along the incision plane. The application of an nJ-energy laser, which can incise the cornea without inducing significant damage to cells and wound healing reaction, offers great potential at reducing scarring following incisional laser stromal surgery.