To establish a town, do you need flatten out all the areas you want to include in your town?

Also, after I flatten out the area, will there be a problem if there are random blocks above the ground that I flattened out?

Also, I am currently building a decent sized structure, and I already dug the ground to bedrock level in some areas. I surrounded the structure with a "glass case" made of glass blocks. If I want to include this structure and the area around it when I use the town plugin, do I need to make a "cut" in the middle of the structure so that there is a "ground" level that connects it to the outside of the structure? I am aware that my description of my "structure" may be confusing. If you want to, you can /warp ant-view to get a better idea of what I am talking about.

Towns do not have to be flat, you just have to mark the corners and everything inside that will be included from bedrock to sky.