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Several barriers exist to the development and optimization of high frequency Micro-Electro-Mechanical (MEMS) resonators, primarily adequate control and understanding of dissipation phenomena. There is growing experimental evidence that anchor losses, which contribute significantly to damping, almost always appear mixed with other less understood surface and interface phenomena on which intensive research is currently focusing. A reliable, large scale and native 3D numerical approach for estimating the anchor loss contribution in general is hence a much demanded tool. In this paper we discuss the implementation of a PML approach to simulate dissipation of waves radiated from the anchor into the substrate. Next we employ the codes developed to perform extensive benchmarks against analytical solutions and verify the applicability of commonly adopted simplifications.