In this paper, we studied the effects of subsurface femtosecond laser micromachining on surface morphology in hydrogels. Depending on material properties and writing conditions, we found surface bumps when materials were hydrated, and trenches when they were dehydrated, which can be attributed to the localized change in water concentration. Such wavy surfaces by laser-induced refractive index change are not desirable in clinical contact lenses. Therefore, the minimization of surface bumps is necessary to ensure the user eye wearing comfort. In addition, we examined the optical effects of the surface features using interferometry and the surface morphology using profilometry. Finally, we proposed a simplified mechanical model based on localized swelling.