So, are you saying that your motherboard has a USB 3 header, but your case only has USB 2 ports on it and you want to be able to use USB 3 devices with them ?
If this is true, then yes you can swap out those ports easily if they are attached with screws or drops of hot-glue.... you may be able to find a set of replacement ports that have the motherboard cable already attached, or you might need to buy the cable separately....
FYI, I have 2 sets of the screw-mount type with the cable attached, which you can have for the cost of postage if you want them