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Hello Ruzan,
The issues you’ve described are related to meshing, a fundamental aspect of the FDTD algorithm. Both the representation of the object and the simulation results strongly depend on the mesh. When using auto-mesh, FDTD aims to maintain a specific number of cells per shortest wavelength in the simulation (within the material). The auto-generated mesh structure changes with geometry modifications, but not every change can be finely resolved by auto-mesh.
The resolution of the index monitor is determined by the mesh size used in the simulation. If you’re viewing the index preview result (before running the simulation), keep in mind that it doesn’t account for conformal meshing or Yee grid offsets. The index preview is optimized for speed and is useful for confirming the basic structure but doesn’t provide an exact representation of what the solver will use. When visualizing the index from the IndexMonitor in Analysis mode, the results depend on the spatial interpolation setting under the Advanced tab.
To achieve reliable results, consider increasing the mesh density and conducting convergence testing.
 Please check follwing references:
1.      Selecting the best mesh refinement option in the FDTD simulation object – Ansys Optics
2.      Understanding Mesh Refinement and Conformal Mesh in FDTD – Ansys Optics
3.      Refractive index monitor - Simulation object – Ansys Optics
4.      Convergence testing process for FDTD simulations – Ansys Optics
Best regards,
Kirill