Me and my brother have 2 houses on 1 lot in rural area and want to refi but told that this does not meet Fanny Mae rules. Help Me?

Have you thought about splitting the lot? Is one house in a llc and the other titled as a residence? I would contact a local mortgage broker in your area, or possibly a credit union.

Do you have a current loan on the property? If so, call the current lender to see what they can do. If the home is paid off call the past lender and talk with them about lending options. If a conventional lender can not provide lending you may have to go to a Hard money or sub prime lender.

Commercial is not a bad idea actually, however they are going to most likely want them as non-owner occupied. Look at Jesse's answer also, that is worth a try as well.

I may have an option but it would depend on the appraised value how much you need to borrow. Otherwise, possibly a lender that specializes in rural properties, or a smaller local bank that is only in your area and makes direct loans rather than Fannie/Freddie backed mortgages.