I'm assuming you mean the difference between these:




I've never really figured out what the deal is with that.  It seems that the more complex the objects are means that it won't have a solid interior when you cut.  In that case, I tend to click the radio button for "Cut" under "Parameters" of the boolean operation instead of just "Subtraction (A-B)".  This leaves the mesh there, but cuts the polys in the shape you want.  You can then extrude the correct polys however you want.  After every boolean, though, make SURE you "Selected Weld" the vertices so that you don't wind up with the dreaded "collocated vertices found" when you export!

You guessed right Travis! Thanks for the answer. It was a shot in the dark, whishing there was answers..

Well it is strange in a way that If you flip that object, you get the invisiblae faces to be visible. so actually you need to just flip the invisible then?

Ugggh ok back to work!