In this work, we present first experimental results on the micro-structuration of monocrystalline strontium titanate (100)-SrTiO$_3$. A self-organized structure appears on its surface due to irradiation with 0.71 MeV/u $^{129}$Xe$^{23+}$ and 0.55 MeV/u $^{136}$Xe$^{19+}$ swift heavy ions at room temperature and under grazing incidence. The resulting wave-like structure appears normal to the direction of the ion beam. X-ray diffraction (XRD) and transmission electron microscopy (TEM) analyses were undertaken to probe microstructural properties below the surface, revealing in particular surface amorphization at high fluences. Such amorphous surface layers, further irradiated at high fluences, may lead to an anisotropic plastic deformation (hammering) effect, inducing the observed self-organized structure due to the grazing angle configuration. This surface morphology was characterized by atomic force microscopy (AFM). A dependency of the periodicity as well as the width of the undulations on the irradiation angle was found as they evolve in the same way. As the ripple formation depends on the irradiation parameters, the characteristics of these patterns can be controlled and thus opens the possibilities for custom surface structuration.