Hello Iokesh,
I would need to see your design in order to provide the most relevant answer. If you could zip up your design and attach it then I can review it and see what may be the issue.
Without the design I will provide some feedback where I suspect the issue might be. Depending on which tutorial you are working from the atoms (the rods, what you want to be holes) and background material are set to:
– Atoms: WG_Example (channel) and WG_Example (material with n=2.5)
– 2D and 3D background: air
If you use the typical default values presented then you are going to get dielectric rods in air. To setup your simulation set the background of the simulation to be air and then set your atoms to a channel profile (One you create in the profile designer) that is air.
Scott