Hello Lokesh,
I had a chance to review your design and you will be relieved to know that your air hole design is in fact an air hole design. I believe where the confusion is coming from is that when looking at it in layout view it appears the same as the rod design. To really see what your discretized material looks like you can use the tab labelled “2D Refr_Idx-Re(y)” where you will see you have a background of 3.47 and an array of air holes, I have attached pictures of both views. Hopefully this clears things up for you.
Scott