You can't as I'm pretty sure that the fixing bolts are under the roof lining, and even if it was possible you would be left with multiple holes in the roof.
We decided to have them removed at the order stage...mainly because I think it looks a lot nicer but also because, should we need to use a roof rack/box, suitable roof bars can be purchased.
I would have thought taking them off would damage the roof. But they are part of its character which has been said, its like taking the airbumps off and filling the doors to smoothe them out. Why???. Also how do you put after market roof bars on nowadays. Last time I did that was when cars used to have a gutter to fix to. Out of curiosity how do they fix nowadays ?