To exclude scenery objects:
If your using FS2004, goto Avsim and search the library for 'excbuilderv2.zip', a small program that allows you to easily build a  .bgl file to exclude objects from a defined area of your scenery. Also get the tutorial. 
Easy to use and connects to the Sim using the 'fsconnect.dll' module. ( The same way as AfCad connects to the sim using FSUIPC)
If you do need to 'flatten' an area, go here, 
http://www.fs-traveler.com/resources-g.shtml, for a small program that will build a .bgl file to flatten an area. Also uses 'fsconnect.dll' to connect to the Sim.
Dave
		
 
		
			
At that time [1909] the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation.          Igor Sikorsky
I intend to live forever....so far, so good.         Steven Wright
You know....you can just rip up a to-do list.