I searched google and found a list of hidden directories and files in OS X at http://www.westwind.com/reference/OS-X/invisibles.html but .file wasn't listed. The file is 0 size and looks like this
---------- 1 root admin 0 Aug 24 2013 .file
Running McAfee virus scan there were over 700 additional files that were Not Scanned because they were protected.
- /Library/Application Support and others