Replacing the microfilter may help for a while but the root of the problem is a bacteria growth on the evaporator which is not easily accessible to clean. . The best thing to do (and its also what BMW recommends) is to use a treatment that has enzymes which will eat away the bacteria. After doing this its best to replace your microfilter and as someone mentioned in the other post turn off the AC but leave the blower fan on for the last 2-3 minutes of your drive to let any condensation on the evaporator dissipate.
Your BMW dealer should sell a treatment for the evaporator but if you decide to DIY then there is a DIY at
www.bmwtips.com for the e39 5 series which is basically the same as x5.