Running a project on top of Windows

Without going into unnecessary detail, what I have is a plane with holes in it. I want the plane to block input, which it does naturally, but I want the user to be able to select anything that is inside one of the holes, like say, an icon on the desktop. Essentially I want an app that blocks parts of the screen, but not other parts, and runs over the top of everything. It would be as if I put a physical object on a touchscreen, for example, allowing me to touch some things but nothing that is underneath the object on the screen. Is this even possible?