How to clear a location or a dungeon in Skyrim?
Some locations on the map will show the tag “Cleared” under their name once you have:
- Completed all the quests associated with a location
- Killed every enemy
- Discovered every hidden passage
- Opened every hidden door and chest
- Solved every puzzle
If you have done all above and it is still not cleared, that usually means there is a quest associated with this location you have not discovered yet.
Search for that location on http://www.uesp.net/, good source of factual info.