The lid comes off with the box. Make sure you get all the bolts. There's 13 total (for the short box, you may have more...) for each box that have to be removed. On mine there are two at each end on top by the hinges, two by the latch bar inside, four on the bottom and three on the inside wall.
You also need to disconnect the wiring for the lights. There's a connector at the rear of the box inside the fender.
Once you've got all the bolts out lift gently by the lid and rock it, again gently, front to rear while pulling up. It doesn't want to break loose the first time you take them out. Just be patient and go easy.