drop the head liner, the nuts are on the inside of the truck. So all the A-B-C-D pillar panels, seat belts, etc have to come off to drop the headliner. Along with the dome light, visors, front lil console thing, etc.
Its a 2-person job to drop and finally remove the headliner out the BACK of the truck.
Then if you are totally removing the rack for the "smooth look" than you need to put duct tape on the INSIDE of the truck, then seal the wholes with silicone. There will be spaces in the roof drip rail moldings. They can be filled in with another set of roof moldings that you cut down.
Rob