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Oh right. Well the clamshell design does help protect the screen when it's not in use. I know the 3D effect works from slits in the screen projecting different images to each eye so the protector probably would dampen that experience.
I guess that either special screen protectors will be made for it or that the screen protectors won't interfere with the 3d because of how it works. I heard something about the smudge problem being the reason why the touch screen isn't in 3d, but I don't really know. ---