Hi Ceshi,
You can use 2D simulation region if the structure has a translational symmetry along one of the axes. In your case since the structure is not uniform along the third axis, a 2D simulation region should not be used. If it was a hexagonal prism of infinite length then 2D FDTD would have been accurate. So, for 2D simulation you can assume that the structure is infinitely long and uniform.
Regards,
Amrita
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