This is a commandline app, which takes the exe name as argument. So you create a shortcut to this exe and add "<space>cmd" (without the quotes) at the end of the Target field of the shortcut. So it should look something like this:
Then you open a command prompt window and double-click the shortcut. The window will be glassed as shown above. If you want notepad then add "<space>notepad"
As to how you should "black"-ify your app window - that I leave it to you. Maybe some other developer will come up with a masking mechanism ,maybe, to allow users to blackify specific portions of the windows, on a per app basis. [If there weren't some fucking exams coming up then maybe I could have devoted more time to it]. If you want source code then pm me, but I wont give it to every tom,dick and harry.