pinched seam question

After stripping paint off I have found that the trunk lid and hood have rust inbetween the seams where they are pinched together. This stuff has got to go. Are these just pinched together? I can't find any spot welds. All I can see is the seam sealer that is holding them. I remember seeing a tool at Eastwood for door skin seams. Will that work here? Any info would be great before I start prying:D .
 
I also forgot to mention that the last IDIOT that painted the car put bondo over the drain holes. I always thought they put those there for some reason. As I go deeper this car has PI (previous idiot) all over it. When I get done with this car I should be able to write a book about the horrors of previous owners.