What type of clearance did you have? If its only secret or below, all they did was a national agency check in which they look at your police and travel records. For example, if you had traveled to the old Soviet Union a few times, that might raise a red flag. With that, its highly unlikely that they would have anything on you that you wouldn't already know about.
If you have a SCI access clearance (access to sensitive compartmented information), they go back 15 years, and they interview people that know you based on people you list, and others. For me, they went to my fiance at the time, a school teacher I had as well as a few friends and parents of friends. If this was what you had, they might have files on you, but if there were anything bad, you probably would have found out about it already.