To save folders, look for the "Folders" button across the top. Once there, place a check mark in the box next to the folder you'd like to download. From the pull-down menu marked "Choose Action" select "Download Folder." This will download your folder to your harddrive for archiving.
Single messages may be saved individually. Click on the 'Save As' link when viewing a message as highlighted below - you can save the file as a .eml file. You may also save it as text messages as .txt files but may lose some formating.

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