This week's book giveaway is in the Other Open Source APIs forum. We're giving away four copies of Storm Applied and have Sean Allen, Peter Pathirana & Matthew Jankowski on-line! See this thread for details.
Is the Unix file system mounted to the Windows box as a separate drive? If so, you should be able to do access files the same way you do local files on the C:. If not, does the Unix box provide an FTP server? Or are the files available via HTTP? Java provides some tools that allow you to handle files over these two protocols. There may also be some third-party tools that will make it easier, but I don't know of any off the top of my head.