Actually, there is a SEMI-easy way of doing this.
Download FSSC (Flight Simulator Scenery Creator) from here:
http://www.fssc.avsim.net/Read a little about it. There's a tool in there (I can't remember what its called, exactly) that allows you to "flatten" a piece of ground, meaning you remove everything but the actual ground in that area. All you have to know is the lat/long of the building you want to eliminate, and FSSC will take it out using that tool.
Funny Flying!
Locke