What they all said about filling holes with Bondo....
If you are trying to "plug"holes, get a thick piece of copper and hold it behind said hole. Weld will not stick to copper, then weld the hole shut and grind it. Now if there are tiny pin holes in the weld you can fill them with body material like metal fil or bondo.
if it is a LARGE void I would cut a piece of sheetmetal and butt weld a patch in.
I welded all of these side molding clip holes shut using the copper method, worked great. You will have to run the piece of copper under cold water every few holes though.