What you want to use for the sending side of your problem is to use MIME::Lite, which easily encodes and sends attachments via mail.

For the receiving side, it depends on how you can automate your Lotus Notes client. On Windows, you can access the Lotus Notes object model, which will give you access to the mail and all attachments easily. On other operating systems without proper RPC/IPC mechanisms, you might have to connect to the Domino server via an IMAP or POP3 interface and then use MIME::Parser to parse out the attachments again.