Particles can also collect on the SI plate, a transparent screen between the focusing screen and pentaprism. It's used to superimpose the red AF flashes on. It may be removed and cleaned but that's best done at a service center.
In my experience blowing air, especially compressed air, into the mirror box, a mounted focusing screen or into the pentaprism usually makes it worse. I learned my lesson long ago! Just live with it and let it be. If it gets really bad scream bloody murder and sent it to Canon for cleaning before the warranty is out.
I've only had the 5D a few weeks but I have a big dirt problem in/on the prism view finder. I have replaced the focusing screen with a grid screen and the dirt is on the bottom of the prism (I guess). I've tried a Blower, Sensor Brush, Canned Air & Pec Pads with Fluid...no luck, just moves some dirt around while other particules don't move at all.
I can only conclude that the camera was put together in a very dirty factory.
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