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Laser in situ keratomileusis (LASIK) is the most frequently used technique for the surgical correction of refractive errors on the cornea. It entails the creation of a superficial hinged corneal flap using a femtosecond laser, ablation of the underlying stromal bed using an excimer laser, and repositioning of the flap. A corneal flap with an angled side cut reduces the risk of flap dislocation and infiltration of epithelial cells and confers unique biomechanical properties to the cornea. A new laser software creating three-dimensional (3D) flaps using a custom angle side cut was retrospectively evaluated, comparing optical coherence tomography 3D (with intended 90° side cut) and 2D flaps (with tapered side cuts) as well as respective intra- and early postoperative complications. Four hundred consecutive eyes were included, two hundred for each group. In the 3D group, the mean edge angle was 92°, and the procedure was on average 5.2 s slower (<i>p</i> = 0). Non-visually significant flap folds were found in thirteen eyes of the 2D group and in seven eyes of the 3D group (<i>p</i> = 0.17). In conclusion, the creation of a LASIK flap using a 3D femtosecond laser cut, although slightly slower, was safe and effective. The side cut angle was predictable and accurate.