The clean up is still going on in Houston and little by little we are making headway. The CDC has a list of steps and recommendations to follow when cleaning HVAC systems. Remediation of water damage in your home is definitely the first step anyone should take who took on water. After a complete water remediation a home owner may want to think about having their air ducts cleaned. Here is a booklet for the steps to clean mold and water damage in your home. This booklet is published by the EPA flood_cleanup_and_the_air_in_your_home_booklet_ . The EPA and the CDC both advise using an N-95 breathing mask to protect yourself from any airborne mold spores.
Here is a link to the page of the CDC that takes a homeowner through the steps of cleaning an HVAC system. If you had mold growth and you ran your AC you may want to have the ducts cleaned.