Archiving emails in folders on macmail

Hi there, I have around 100,000 emails filed in folders (and folders in folders etc) On My Mac in MacMail. I cannot find a simple way to archive them in their current folders. The only way seems to be to archive each folder individually and save them into a folder with the same name to preserve the structure. I would prefer not to use the mbox system so I don't have to reinstall them onto my computer to search them. Any suggestions?

And why can't I find mail in the topics?