Sure, run the command [unfreeze map I believe.. or open [Admin gump, select the World Building page, and there should be a button to unfreeze the statics for the entire map.
You will then need to copy the statics# and staidx# files (where # is the number of the map you are working on) and replace them in your Ultima Online folder. Now relog in game.
That will take some time depending on how fast your computer is.. 5 minutes, to even an hour if your PC is old.
You will not want to just clear the facet, because you will also wipe the water transition tiles that are up against the land tiles.. the water borders, so from here, you may want to take some time and just run around wiping areas by hand or boundry box areas. You could also run commands wiping specific item #'s. like.. [facet delete where itemid #### I think would work.. might not be exactly the command, but you get the idea. take your time, and you can get great results.
The faster you try to run a command to clear areas, the more you will remove that you will realize you wanted to keep though.. just to keep in mind.
Im sure there are more ways, or better ways too.. but thats one way to do it using the client, not third party tools.