Without seeing it, I would have to guess it isn't a closed polyline that is being extruded.
3D modeling is the way to go. If you don't need it for this job, you might need it if you decide to change jobs later. Many errors can be reduced by drawing in 3D because you do not have to picture the sides, top, or bottom in your head when dimensioning it in paper space. Some things you might overlook in your head can be easier seen when it is modeled "in real life." At an old job I used to work at, everything was still drawin in 2D. On one job alone there was $70,000 worth of mistakes because one of the drafters didn't forsee interference between some parts, and misaligned holes on other parts. Multiply some small mistake by a run of 500 units, and the problems added up quickly in dollar amount.
Give us more detail if you are still having problems with your drawing.