I doubt he can Transfigure antimatter. If he can, the containment will be very hard to get right, and he would absolutely have to get it right. How do you even stop it blowing up your wand, if you have to contact the material you're Transfiguring?
Transfigure the containment device first. Then find a way to transfigure the antimatter inside it. To solve the wand contact problem, transfigure the empty container into a full container. Then his wand is in contact with the container, but the container doesn't actually change.
Granted, it's extremely dangerous, especially when practicing.
Yes, there is the problem that no-one knows what containment for macroscopic amounts of antimatter looks like. We have some ideas, but nothing that would be safe for Harry to try.
This is a new thread to discuss Eliezer Yudkowsky’s Harry Potter and the Methods of Rationality and anything related to it. This thread is intended for discussing chapter 98. The previous thread is at nearly 500 comments.
There is now a site dedicated to the story at hpmor.com, which is now the place to go to find the authors notes and all sorts of other goodies. AdeleneDawner has kept an archive of Author’s Notes. (This goes up to the notes for chapter 76, and is now not updating. The authors notes from chapter 77 onwards are on hpmor.com.)
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system.
Also: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: