The exercises mentioned in this article are good ones for treating flat feet. There are also many other exercises that build the inner foot muscles so with a little research I'm sure you can find one that works for you.
In addition to exercise, you might want to try a good pair of orthotic shoe inserts. Some people who use them report a world of improvement in regards to the pain they experience from flat feet.
There are also specific shoes for flat feet, and there are some styles of shoes that people with flat feet should never wear. Flip flops would be a good example of what not to wear if you experience pain from flat feet. If you notice more pain than usual when you wear a certain pair of shoes then this should be a hint for you to consider removing them from your collection.