what I want to do is remove/delete the email I read..and so far I haven't found a way.

Do you have access to the mailbox via POP3? In that case, using Net::POP3 makes it easy.

Otherwise, if you insist on doing this with file operations: IMO that's risky, with multiple processes accessing the mailbox at the same time — new mail arriving, for example. Be very careful you get the file locking right.