Originally posted by GunsForBucks:

Stone flooring will cover them.
I kind of like that they can't be destroyed... some things you might think you have enough of may end up in short supply later due to new recipes.

I'm the opposite. I really wish flattening terrain removed the spawn points for things like branches, flints, plants and rocks. Maybe for branches it could be based on taking down the nearby trees idk. I'm not worried about running out of anything really, given how massive the map is. But I'm soloing so maybe it's a bigger deal on accessible servers.