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Your skin should return to its normal status after it is healed - it is not a good idea to put a band aid on the skin that is healing as it could increase the risk of infection, although it is unlikely that this would cause a problem if you did it only once.
I would avoid putting a band aid on the area that was just treated with Fraxel. The skin can be irritated or pulled off and you can have the possibility of a scar.