I am very new at this, but i want to make an airport of my own. I got Afcad and i have been messing around with it making the various taxiways and such. I ran into a problem though, i rebooted fs9 and it generated the scenery(all good so far) when i went to the airport i found that parts of the runway were submerged in the ground where some parts werent. I was wondering if anybody could point me in the right direction as to a program or maybe a method to solve the program. I have looked at some tutorials but i havent seen anything that really pertains to my exact problem. Can anybody help me out?

I think you need to make a flatten around your airport. This will make sure that the area of your aircraft all has the same altitude.FsFlatten is a tool that can help you in making the flatten (http://www.fs-traveler.com/cgi-bin/fstutilities.zip), but you could also make it with tools like Ground2k or SBuilder of course.