The best way to do this would be to convert your duplex to condo's. You should get a real estate lawyer and title company involved to do so. You'll actually need to set up a condo association to make it legit. This was a popular method about 4 or 5 years ago. Although, lately it's been harder to get financing on half duplex condos. The lenders typically require some money in association reserves. It's definitely worth looking into though.
You certainly can sell them separately, the prices are down on them now though! I do have a client looking for a whole duplex, this could possibly work for them! Call me if you'd like to talk about it!