I found this and talked to a friend that does flood damage and mold remediation,he say it works...
I hope it works :)
Greg
Mildew Smell in Flooded Car
If you smell mildew. chances are there is still moisture in the car. Use DampRid to suck up any moisture and it will also remove some of the odor. You can buy DampRid just about anywhere, like Walmart in the house cleaning products isle. Bleach is the most effective way to remove mildew but I dont think you want to use that on your interior carpet. Sprinkle baking soda on the carpet then spray it with vinegar and water and watch it fizz and eat the mildew away.The vinegar smell will disapate after it dries. These two combined work miracles on everything!!
Remember, if you smell mildew, there is probably mold in the car as well. The spores can get into your daughters lungs and cause upper respitory problems like stuffy nose, conjestion, mucus build-up, headache, and a general ill feeling. The safest way is to have the interior carpet replaced. I just went through a similar problem with my car after all of the hurricanes.