Removing them individually is the way to go. For doing repetative stuff like this though, I typically use Imacros. You can record the event of removing a user and then configure it to be replayed and remove the remainder of users.
Not an official 'Atlassian' method by any means, but an effective way to do some browser automation. Imacros is a firefox plugin that you can use to automate stuff in your browser and it's free.
This may not be the answer you were looking for, but if I had around 100 users to delete I would do this:
1. Write a SQL report to display users who have not logged in recently.
2. Extract those usernames from the SQL report.
3. Record the following event in confluence (Search for the 'username' > delete user) This will give you 2 lines in Imacros for every delete.
4. I would then wrap the code around each username that I pulled out of SQL. This would give me 2 lines in IMacros per user deletion.
5. Run it to delete only the user names specified from the SQL report.
This obviously assumes that you have access to SQL and can easily wrap some code around the username section of the Imacro recording using excell or something. Hopefully all that isn't too confusing.
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