Handling the fish is not a good idea, especially an ill fish. Human skin may rub off some of the fish's mucous coating. These, like many other tangs, have a thin mucous coating to begin with.
The 'holes' are open sores. These are places where opportunistic bacteria and fungi can infect the fish. The water being used for the TTM needs to contain an antibiotic. I don't know what you have in your fish 'medicine cabinet,' but I'd recommend Kanaplex.
This fish needs extra help in nutrition. Look at the
Fish Nutrition post. Add supplements to this fish's food according to that post's recommendations for an ill fish.
Keep Kanaplex in the water at therapeutic levels while continuing on with the TTM.
I cannot tell more from the photo. I'd prefer to see a long (1+ minute) video of the fish under white light or under ambient room light. I don't see where these 'holes' may have come from. They are sizeable and it's hard to imagine that they 'just appeared.' More background may be useful like: How long have you had this fish? Are you sure the fish has a
Cryptocaryon irritans (Marine Ich) infection? If just acquired, where did the fish come from?
I have never been much of an advocate for the TTM. It seems unnecessarily stressful on the fish and hobbyist.
Ask if you have any questions, I'd be happy to help.