Position a stepladder a few inches away from the Explorer. To make your work easier, place the ladder in the middle of the rack.
Climb the ladder and look for Phillips-head screws holding the roof rack in place. These screws would be installed along the middle of the rack rail and should be around 3 to 4 in number. With a Phillips-head screwdriver, remove these screws.
Now you need to remove the screws at the other side of the roof rack. Move the stepladder and place it on the other side of the Explorer. Remove the screws on the other side of the Explorer the same way you did in the earlier step.
Once you have removed all the screws, simply lift the cross sections of the rack and carefully set them aside.
Now it is time to remove the inner rails. Use a Star wrench for this purpose. For an average sized roof rack, there should be about three to four rails that you will have to remove.
Wipe clean the roof to remove the outline of the rack. Use a clean piece of lint-free cloth for this purpose.
Attend to the holes where the screws were previously installed. Fill them with silicone. This is important to prevent water from leaking into the vehicle through these holes. To make the silicone patches less noticeable, use touch-up paint the same shade as your Explorer.