Oh man, you have got yourself a potential money draining situation. Hopefully no one is getting sick from the mold, if not, time is on your side, you'll need it.
You could end up with the guy with a shop vac and some brushes that does nothing to a full five alarm mold remediation crew that goes door to door in your neighborhood sounding the alarm of MOLD!
I agree with Mike, it's unlikely to be a filter issue. Sounds more like a moisture issue in the vents. You need to figure out what's causing that because the mold will be right back even with a thorough cleaning.
Finding a good company to clean the vents (after you find your moisture problem) is going to be hard. The industry is 95% crackpots. There is a certification body, forget the name, that might get you closer. Again, you don't want the guy with the shop vac, you want the guy with the big truck and the huge vacuum. Also he needs to have a fogging machine to treat the vents after the cleaning. Ask what they use for a chemical, they are required to tell you. Benefact is a really strong option that is non toxic to humans and pets, it's used in hospitals and will make your house smell like a hospital for a day or so.
Most of all, if no one is sick, take a chill pill and don't overreact. There are companies that prey on this. Mold is the new home Boogeyman after lead paint and asbestos were pretty much gone. All mold isn't bad, most mold in a house isn't toxic, but the water it feeds on is the bigger problem. And most scam companies won't fix the water problem, just tear apart things, spray chemicals and leave them for someone else to fix.
And by the way, if you like blue cheese, you eat mold...lol.