Marks that look like acid? What are we talking "burn marks"? discolored areas? what? I would call the dermatologists office and ask them what you can do about these marks - in for a penny in for a pound - meaning you have already invested X amount of energy, time, money to be treated by a doctor, finish off the treatment by having this dealt with as well with the same doctor. Most likely (since I do not know the medicine, but could hazard a guess) this is a matter of time that we are dealing with and other than "cover-up" make-up you have to let it run its course.

Sea shells diluted in lemon juice with will give an ointment which could be useful to get rid of the marks.

The marks are where the skin has become irritated and inflamed by the medication, since many topical preparations for acne (I'm guessing this is what you have, in common with so many others, but the answer is relevant to many other skin complaints) treatment are acidic in nature or have irritating active ingredients - you are waging warfare on bacterial colonies so a bit of friendly fire is to be expected! Firstly, I would advise not to put too much on - from both lectures and from personal experience, too much ends up damaging your own skin as well as the microorganisms present on/near the surface, so your are only killing more of your own skin cells if you use too much product. Secondly, as Athrael advised, go back and see your dermatologist - s/he shoudl be reviewing the case anyway to see how the treatment is working. Thirdly, if you have just started the treatment, these effects are very common, as basically your skin is not used to the product yet. The skin is highly adaptable and constantly regenerating itself, so over time it will adjust and the marks should lessen. In the meantime, if they are dry/cracked as well, try washing your face with a gentle soap and water. Don't rub your face dry, always pat it dry with a towel, and try to avoid scrathcing/rubbing at itchy areas as this can aggravate inflammation. If the skin isn't too red, but is dry, try dabbing a small amount of moisturiser on the area to see if this helps to soothe the area. Don't put too much on though as your skin needs to be able to breathe. If you use concealer, likewise try to use as little as possible, because covering the skin provides an ideal environment for bacteria such as P.acnes to grow, which can compound the problem.