Yes, remove the carbon filter before it removes the medication.
Probably a good idea to replace all the filters, too, once the meds have cleared up the infection on general principles that you don't want residual parasites or medicines in there. If you are relying on your filters as a primary bacterial media, then you will have to change water more frequently to avoid ammonia buildup until you have reestablished sufficient growth to balance the nitrogen cycle.
Temperature also controls the lifecycle of the Ichthyophthirius multifilius parasite; raising the temperature and raising the salinity will help -- do it gradually and only as far as your particular fish can tolerate.