I just pulled all 4 of mine to paint recently, and this is how I did it.
First unscrew all the screws at the end with the mudflaps, I think they were 5/16" self tapping screws, maybe 4 or 5 each flare. Now pull the push pins from the wheel well inner lip. I used a pair of diagonal cut pliers for this, work the jaws under the head of the push-pin and either cut them or pull them out. My cutters were curved, so I could rock the pin out with just a twist of the wrist. They usually need to be thrown away, but if you bring them to your local auto body and paint supplier they can match them I got a whole box with enough push pins for all 4 flares for around $8.00. After all the push are out you need to pull the flares from the sides of the body. The flares are held in place by plastic anchors similar to a push pin located at the outer edge of the flare, they may break off, I lost maybe 2-3 per flare. Again, they are cheap at the paint store. When pulling these loose they tend to sound as though you are tearing the truck apart, but it usually comes off fine. You may need to use a putty knife to start some of them, but be careful not to scratch the paint outside the flare. if you scratch paint in the area that the flare covers be sure to touch it up to prevent rust.
Hope this helps,
John