Ah, I see your problem now. IGES files can be a nuisance. You have a couple options.
The simplest (aka. ghetto) way would be to cut the flange off with an extruded cut down from the top surface then fillet the raw edge to match the rest of the case (or you can do this all in one step by cutting from teh side with a sketch that includes the fillet). This would give you the clean face to add the vent. I'm assuming you don't want the mounting flange in the final model though. This also assumes that the case sides are perpendicular.
The way I would do it though would be to forgo the vent feature tool and draw the vent manually as an extruded cut. to do this you could create a reference plane offset from the outer surface parallel to the case wall. Draw your vent pattern on this new plane and use an extruded cut to the inner surface. This would cut through all the various surfaces and allow you to keep the flange in the end model.
I'm more of a manual Solidworks user, I don't like using the special tools but that's just me. Also, I hate IGES files, PITA!
Cheers