If you want to the user to be able to browse the server with a browser, you'll need to write some server side code (see java.io.File) that reads the contents of your file system and returns them in a form that can be presented in a web page.
You can certainly use JS to open a new window that calls these server side resources. With Ajax, you could also make requests to these server side resources and draw them directly to a pre-drawn page but there is nothing built into either JS or JSP for browsing a server's file system.
I’ve looked at a lot of different solutions, and in my humble opinion Aspose is the way to go. Here’s the link: http://aspose.com