Well, I've just been working on that very thing, myself.  Came in here to ask a question and get one asked of me.

There are a myriad of tools to do this with, and a million different ways to get there.

Right now, I'm experimenting with Ground2k4, which is a small program that can build everything you need on the ground.  I'm using it to edit an island I've been working on.  It can (apparently) rearrange nearly everything, right down to the water or land that is used.

You can get it at AVSim, by searching for "ground2k2" or "ground2k4".  There's also a help file around there.  Just search "ground2k" and scroll around until you find it.