Most scriptoria are in monastery cloisters or at least an above-ground library, to get good natural light. But should for any reason (security, perhaps) you want to have one in a dungeon, here's a good floorplan to use when visiting adventurers probably are not here to borrow a book or two!
It's a simple rectangular room with double doors at each end. However it is made a bit more complex - as the scene for a brawl or chase - by the racks and bookshelves within. There are also two tables, beside which the only light sources are located, at which scribes or librarians can work.
Perhaps this is some reclusive wizard's library, or secure storage for a faith's most holy and valuable texts.
Whatever you decide it is, it makes a good and atmospheric setting for the adventurers to come poking around.