First, are you sure they're actually scratches and not just streaks? You've tried cleaning the screen with a microfiber cloth or other lint-free cloth and not been able to remove the marks? I've been using a smart cover with my iPad and given how it operates can't really see how debris would be dragged across the screen so as to actually scratch, though I can't say it's impossible.
Anyway, if the screen is indeed scratched, you'd have to pay Apple's flat replacement charge, or look for an independent service center to replace the screen. You can see Apple's charge by going here and selecting your country: