Separating offset-ed circles from base surface

Hi! I have a base surface which I have divided in to a grid and have used the center of the grids to create circles. Further, I have offset the circles and now want to separate the offset part from the base surface. The idea is to use the inner part as windows and the external part as opaque so that I can assign separate materials to them and can bake them separately. Any suggestions and help are most welcome.

TIA,

Ram