Rare-earth ion doped potassium yttrium double tungstate, RE:KY(WO4)2, is a promising candidate for the realization of on-chip lasers and amplifiers. Two major bottlenecks difficult the realization of compact, high-contrast devices. Firstly, the crystal can only be grown on a lattice matched substrate, leading to a low (<2×10-2) refractive index contrast between core and cladding. Secondly, the required thickness for the high-index contrast waveguides, ~1 μm, makes a lapping and polishing approach very challenging. In this work we propose a novel polishing stop that will permit to accurately control the final thickness of the KY(WO4)2 waveguide within a few tens of nanometers. A 1 mm thick KY(WO4)2 substrate is flip-chip bonded with an adhesive layer onto a SiO2 substrate. Afterwards a low temperature pulsed laser deposited (PLD) Al2O3 layer - with the desired final thickness of the KY(WO4)2 waveguide core - is deposited on top of the assembly. The sample is then thinned using a multistep lapping and polishing procedure. Earlier work with a polishing stop made from SiO2, showed a decrease of the polishing speed with a factor 3-4, allowing the termination of the process within a tolerance of a few tens of nanometers.