eMail Manager offers 3 workflows for handling attachments when filing messages.
Workflow 1 keeps any attachments within the email when filed. This is the default method when filing incoming messages or in batch file mode.

Workflow 2 files messages and attachments separately. If you are filing the message into the file system you will be asked if you want to save the attachments to the same folder as the message. If you click No then you will be able to browse to a folder to save the attachments. If you are filing your messages to an Outlook folder then you will automatically be presented with a location to save the attachments in the file system.

Workflow 2 removes attachments from the save message and replaces then with a text file attachment containing a list of the attachments that have been removed from the message and filed elsewhere.

Workflow 3 works in a similar manner to workflow 2 when filing incoming messages except filed attachments are left within the message and not deleted.

When filing sent items this workflow changes slightly and will simply remove the attachments replacing them with a REMOVED_ATTACHMENTS.txt file. This idea behind this workflow is that if you are emailing files to people you probably already have those files stored in your file system and may not want to duplicate storage. This feature can be turned off by selecting the ‘Always embed attachments for outgoing message’ option in the settings dialog.
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Note that embedded attachments such as images pasted directly into the body of the message are not treated as attachments and will always remain embedded in the message.
