KY(WO4)2 is an attractive material for integrated photonics due to its high refractive index and excellent non-linear and gain characteristics. High refractive index contrast structures increase light-matter interaction, reducing the threshold for lasing and non-linear effects. Furthermore, high refractive index contrast permits dispersion engineering for non-linear optics. In this work, we present a novel fabrication method to realize pedestal microdisk resonators in crystalline KY(WO4)2 material. The fabrication process includes swift heavy ion irradiation of the KY(WO4)2 with 9 MeV carbon ions and sufficient fluence (> 2.7·1014 ion/cm2) to create a buried amorphous layer. After annealing at 350° C, microdisks are defined by means of focused ion beam milling. A wet etching step in hydrochloric acid selectively etches the amorphized barrier producing a pedestal structure. The roughness of the bottom surface of the disk is characterized by atomic force microscopy.