You can actually dig them up with a shovel, but I think that may take longer and you'd have to keep on digging up the hole again.
Another way of doing this is to pull them out one by one.
Oh, and you could always rebuild town too...
One last thing, Phyllis runs the night shift, so if you walk up to the green matt an ask about the environment she will say something like Trees you need more Trees! Or flowers. And also you can plant flowers, trees, turnips and loads more too at Tom Nook's or buy them from Ol Joan for the turnips.
I do hope this helps and Good Luck!