This is not a direct answer to your question, but a while back I had the need to parse a mailbox and I used a few perl modules to accomplish this task: Downloading IMAP Folders to mbox file. This is how I open the mbox file via IMAP.

What I would do is to write an interactive script (if you want to go through the mailbox email by email) that will open up a connection to the server or the mailbox on the server and ask you to keep or delete it based on the subject of the message (which is easy to extract using Mail::Box::Manager (Example: Re: splitting email messages from /var/spoolio... or Re: sorting email with email::folder).

Without knowing more about your setup (Exchange server or linux server using dovecot/courier with postfix/qmail/sendmail into mbox/maildir mailboxes etc) it is difficult to provide you with any more information.