The only way to remove trees, would be to edit the map files with Centered+ to delete them, and use those files on both the server, and every client who logs into your server.
tl;dr It's not easy, so if you are looking for an easy way, there isn't one.
RunUO system emulator (also ServUO) can work with static files. This means that you can do it without external programs. Use freeze and unfreeze commands.
