In FS9 I used to use a program called "excbuilder". It worked with simconnect to sync with FS9, then you just slewed to an upper left and lower right point encompassing the exclude area and it would compile an exclude bgl. It was pretty simple to use, but that was years ago and I don't even know if it will still work with the newer OS. I think I was probably using XP at the time.
I know it's payware, but AFX is an excellent program if you plan to do a lot of airport/scenery design and especially if you have both FS9 and FSX because it's compatible with both and doing excludes and flattens is very easy inside that program. You can also use Scruffyduck's ADE Program which is free and has come a long way since it's rough beginning.:salute: