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Rare-earth ion doped KY(WO) is a well-known active laser crystal, due to its excellent gain characteristics and its relatively high nonlinear refractive index. As these properties are of great benefit to applications in integrated photonics, a study has been done into the fabrication of high refractive index contrast slab waveguides in KY(WO) as a first step towards the fabrication of channel waveguides. When properly choosing the fluence and annealing parameters, ion irradiation with 12 MeV carbon ions produces a step-like damage profile. Confocal Raman microscopy, X-ray diffraction and transmission electron microscopy are used in this work to study the structural damage induced by ion irradiation. The characterization indicates damage to the crystal structure due to the ion irradiation that increases as a function of both depth and ion fluence till the threshold for amorphization is achieved. Successive annealing steps of the irradiated crystals at different temperatures show partial repair of the crystalline structure when the irradiation did not fully amorphize the material. When the threshold of amorphization was reached, annealing further increases the damage induced by the irradiation. By tuning the irradiation fluence, a high-refractive index contrast slab waveguide in KY(WO) produced by ion irradiation was demonstrated.