How to remove all lead to allow welding?

Not sure if this would work for your issue, but I've had success filling holes this way...

Put a screw in the hole, but not all the way down to the screw head
Tack weld it in a couple of spots so it is secure to the metal
Grind it off flush
Use filler to smooth over the area

If it is a small hole(s), then you can easily just use fiberglass filler like Lee Robinson suggested.