the only way to to get thistles removed is the use of of the devcommands (cheats)
there is a command that removes allmost everything in a given radius around the character

forcedelete #

(# stand for a number from 5 to 20 meters around the player)

use this with caution!
i recommend using this when you need a cleaned space for building use this before you start building (otherwise your placed objects might get destroyed/removed)
this command removes spawables like thistes permanently within the given radius
no branch, rock or another spawnable will stick thru your floor again

removing rocks might need to execute that command twice

dont dive into cheating too much as this might influence your game experience