I recently asked a question on Math.SE and got an answer. However, I wanted some clarification so I wanted to add a comment. However, I am unable to use the @username feature to make sure that the answerer gets to know that I had requested some clarification. I have tried to edit and even post a new comment. I type @username and then my comment. However, when I press "Add Comment" Button, the @username simply disappears and only the main comment body appears in the comment.

Could someone explain what is going on and how can I notify the answerer?

If your comment is to the author, the @-usernames will often be removed since the author gets notified of all comments anyway. Only if there are others commenting, and there is some chance of confusion, will the system leave them.
• As the question shows, there is added chance of confusion from the system deleting part of our comments, and there can be ambiguity as to whether the comment is intended to be directed toward the user who posted the answer or a more general comment (or whether it was directed at a comment that was subsequently deleted, or hidden after more than 5 comments). When my comments are directed at a particular user but the @ thing is deleted, I will often just add [userneme]: to the beginning to remove this chance of confusion. Jul 23 '13 at 18:47
• @JonasMeyer: the only @-name that should ever be suppressed is that of the author of the article being commented on. If I see a comment without an @-name, I assume it is intended for the author.
• just to further clarify what @robjohn said: the replies feature also allows for the author to respond to the comment without using an @ symbol when there is only one commenter. That is to say, robjohn's first comment in this thread would also arrive in Vishal's inbox. Obviously robjohn's comment was talking about commenters other than the author himself (if would be strange for the author to talk to himself... though it has happened.) Jul 24 '13 at 7:31