Autocad headers help

[ALLstrokedOUT]

Hello everyone,
I know that AutoCad isnt the best program to be doing this but im basically being forced to use it for a class im taking here at USF..

Weres supposed to make a 3D rendering of anything we want, as long as its complicated enough. I decided on a set of headers for an LSx. heres a couple pics of where im at:


Can someone help me figure out why the flange is filling the holes when i extrude it and not the actual part? (its AutoCad 2009) thanks in advance guys!