It's not the AF screen and has nothing to do with AF functionality. That is done though the mirror by the AF unit in the bottom of the camera body.
The ground glass focusing screen which you're talking about can be removed from cameras for cleaning purposes, however that doesn't necessarily mean that that is where the dust is. I see specs in my viewfinder although my focusing screen is spotless, these are somewhere either on the pentaprism or further up in the viewfinder mechanism. Realistically if you dismantle the camera looking for these specs the chances of something going wrong (such as scratching the focusing screen when releasing the retention spring with a screwdriver) are far greater than the potential gain (one less spec in the viewfinder which doesn't affect the camera's resulting images anyway.