It is well known that the femtosecond laser lamellar cut induces some degree of surface roughness. Nevertheless, as in femtosecond laser-assisted LASIK (FS-LASIK), an excimer LASIK ablation is performed, and the post-ablation stromal bed should show some degree of smoothening. We decided to compare, using atomic force microscopy (AFM), the roughness of the corneal stromal bed, after a femtosecond lasers device flap was created with or without an excimer myopic ablation. Using 6 freshly enucleated porcine eyes, we created in every eye a flap using a femtosecond laser. Additionally, in 3 eyes, an excimer laser ablation to correct-3 diopters (D) was made. AFM imaging of the remaining corneal stroma was performed. Ten different square areas of 20μm x 20μm at the central area of the stroma of each corneal sample were studied. The roughness parameters used were the root-mean-square deviation from a perfectly flat surface. The RMS deviation was 360 ± 120nm in femtosecond laser only, and 110 ± 20nm in those cases where excimer is also involved (p < 0.0001). Our results show that the roughness of the surface treated with excimer is clearly lower than in the group with no excimer ablation; thus, the application of laser excimer after a flap created by femtosecond laser seems to soften the nano-irregularities created by this technique.