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I had a similar situation happen to me a few weeks ago and used a dehumidifier to get rid of the musty smell and then cleaned the floors down with a mixture of baking soda and white vinegar.

After the floors dried I went back and mopped with an all purpose disinfectant, which is made of 4 cups of water, 5 drops of natural soap, and 30 drops of tea tree and/or lavender essential oil. The essential oils have disinfecting properties.

I would recommend an energy star dehumidifier and using the collected water for plants, car washing, or whatever else tickles your fancy.

Flooding that comes from backed-up sewers, hurricanes, flash floods that affect sewers etc bring biological contaminants that flooding from busted clean water pipes and basic rain leaks don't. Basically you have to treat it like you would toilet water AFTER you used the toilet to put it bluntly.

Contaminated water should never be reused, the area should be disinfected (not green I know, but bleach is a standard and safe remedy), and anything porous should be discarded.

Try looking at the recent news coverage for Louisville KY (like the Courier-Journal) for some flood cleanup information or past coverage of Katrina etc.