It sounds like you're referring to the viewfinder focusing screen - it's the "ceiling" to the mirror box. And it's plastic, not glass. A few smudges won't affect anything at all, other than the view you see through the viewfinder. No impact on photographs whatsoever.
It's easy to remove and clean, and if it has scratches that can't be cleaned, it can be replaced.
The best removal/reinstallation instructions I have seen are here:
--Pentax K5/K7/K10D/K20D/K30/ISTD Focusing Screen Installation Instruction--
To clean it, I'd suggest standard drugstore 70% isopropyl alcohol on a soft, lint-free cloth. I have done this before, and it gets most stuff (fingerprints, etc.) off pretty easily. But because it IS plastic -- be very careful to avoid scratching it.