Is this because you want new ores/trees to be in an existing world?
Last time i used MCedit it had a feature to repopulate chunks. This mantained the landscape but runs the ore gen code on it again.
I had an existing mineshaft system, repopulated it, and the walls of the tunnels I had dug were lined with new ore, as it didnt change where the existing blocks were.
The only problems with this are that it spawns new water and lava source blocks in anything that could be a "cave", and Im sure you can see the problem when the world gen decides that the chunk right next to you base is perfect for a RP2 volcano.
Back up the world before obviously, or you too could be digging your base out from under a basalt mountain full of lava.