WICruiser,
The size and shape of the hole (s) you are wanting to fill/patch, as well as the desired finish, will probably be the driving factor on method or material used. Most hardware stores carry round metal spring clip caps to press/snap into various round hole sizes. An alternative could be something like JB Weld Paste (ExtremeHeat). The list goes on. Others may chime in on what they found that works.
Maybe pictures of the nefarious holes would help???
