As you can see, I have vertices on top of vertices, I'm trying to delete them using delete doubles but it says there are 0. But they're clearly overlapping perfectly. I set my merge distance to 0 but they still wont delete. I'd rather not manually delete all of them so if you guys could point out what I've done wrong please help.
I didn't realize you needed to select vertices for remove doubles to have an effect. To remove doubles on the whole model, select everything with A first (you may need to press it twice if you have anything selected beforehand).