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Well.. the correct way would be to weld them up.

But if not, you have other choices, one being the way you mentioned. On one of my previous cars that I debadged, I used metal-to-metal bondo.

Just make sure you sand down all the paint, and put tape and the backside of the holes.

 

If you use regular filler, aka bondo, chances are at one point in time it will be messed up. You can use a metal filler such as liquid metal. Then as mentioned you can weld it which everyone will tell you is the best way and doesn't cost much if you have someone to weld or can weld yourself. I have at one time or another done each of the options and using a metal filler will probably work for you.

 

I had a local body shop weld the holes and paint that part of the trunk lid from the spoiler down.

 

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Yea if you have a welder to do it that is the best solution really. As for the front bumper plastic welding is the way to go.

 

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It would take a long time to rust or anything basically I think you would just end up with a nasty trunk.

 

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Before I had a welder, I figured out a good way to fill holes in body panels on my MR2.
http://www.mr2oc.com/showthread.php?t=315017