During my first round of Master-Cleanse cleansing, I had to go on Antibiotics on or about day 3. I was able to do the cleanse while on the Antibiotics (they were supposed to be taken on an empty stomach, if I remember correctly) & expelled plenty of toxins!
I think you'll be just fine doing while on the medication. I wouldn't suggest not taking the medication to do the Master-Cleanse because I've had Acne problems in the past & know that the minute I stopped my meds, I broke out. I wouldn't want to wish that on you! Good luck!