Can I use URL mapping for File System-indexed documents?

Yes, although it is optional. URL mapping allows portal administrators to create a different URL and map it to portal pages. 

On providing a directory path for a file system collection, URL mapping can be optionally set for each directory.

For example, C:\testfolder can be mapped to http://www.examplesite.com so that even though SearchBlox indexes the content from the file system when a user clicks on the search result, the web document is served from the webserver. The child path would be automatically mapped to the URL.

Example:

/tomcat/webapps/tomcat-docs/

URL Mapping

http://localhost/tomcat-docs/

To learn about File System Collection read: File System Collection in SearchBlox