First, how long has the carbon been in the filter? 2nd, what kind of filter do you have? If the carbon has been in the tank for more than about 2 weeks, you can leave it in the tank, since it's no longer active. If the carbon is attached to the other media (as in whisper filters, for example), then you can not remove it, since this will also remove the bacteria hosting in the media and this will result in a nasty ammonia spike--not what the fish need right now!
2nd, since these are glass fish, I'd forego medication and treat with salt instead. You need to clearly idenfity the problem, but know that glass fish are very prone to getting a viral infection that gives them a fleshy growth that looks like cauliflower. It's not contagious, and seldom lethal, but it indicative of stress. Is the tank cycled?