I don't really understand what is it that you're trying to do, but as far as I know, no, you can't do that.
Oversimplifying, each window draws to a different texture, and the Desktop Window Manager (DWM) composes all of those textures into one big full screen texture, which is what you see.
Generally, the DWM composition pipeline is a core part of Windows, and there are no documented ways that I know of to hook into it to mess with the composition. I am pretty certain this part is extremely optimized to run as fast as possible, and allowing people to hook into it would certainly create performance and stability issues.
It may be possible for a specific graphics driver to allow you to hook into the pipeline after composition has finished, but first: I don't know of any driver that would let you do that; and second: any program you make would only work on computers with that specific driver.
Without understanding what is it that you're trying to do, it's very difficult to give you alternate solutions, but if you want to create effects as screensavers do, you could do as v.oddou says: take a screenshot, and apply any modifications you wish to it, and then drawing it full-screen. Obviously, the displayed windows won't be interactive, since you're just showing a modified screenshot.
What is it that you're trying to do?