Hmm... I don't know why exactly you're not using something like mutt to delete the message manually, but I'll guess that's because you've got a bunch of users all with some spam that's huge. As a sysadmin I wouldn't delete anything from a users mailbox without their permission first though because there's a large chance you could screw something up :)

Shop safety warning aside, a tool that might prove useful is formail (particularly with the -s option). It's probably even already installed on your linux box as it comes with many distributions. You can then use perl to just decide which messages to keep and which to throw away.