You can get specialist soft top cleaners but when I got my new soft top it had a bit of mildew/mould on it, I wiped it down with a warm soapy water mix, waited for that to dry and then got a 50/50 mix of white vinegar and water and wiped the mouldy area's down with that. Did it 3 or 4 times and it has kept it at bay for a while.
I think once it has taken hold it takes a while to get rid, once the warm weather comes along and I can get the dampness out of the car then I'll fully sort it out and re wax the interior. Till then its just a case of keeping it at bay.