Rust - Advice

I have a 2005 Ford 500 with 34,000 miles. I recently noticed that the trunk has some significant rust bubbles starting under the paint. The car is under Ford's extended warranty which excludes rust the dealer smugly pointed out. (Is it any wonder these guys are losing market share?). Anyway, although tempting to flame out about why a three year old car would begin rusting, my question is - Is there anything to be done about this? Has anyone developed a method to prevent rust? Any advice?

Once it starts the biggest thing is to keep all drains open on the rocker panels and anywhere else with drains.
When I lived in Ohio places would undercoat a vehicle which helps. After it has started I would ask around but I'm not sure. You can get the rust spots primed and repainted.
The manufactures can buy metal which doesn't rust such as cor ten made by US Steel but rust helps sell vehicles.

Yes - I will talk to a body shop, I was just wondering if ther was any hope once a car had started to rust.
Thanks for the reply.