Hi,
It is recommended to install all the Symantec features AV / PTP/ NTP with latest definitions.Always make sure that your computers are receiving definitions regularly. Did you installed NTP as well?
It's also recommended to use latest SEP version i.e RU7 MP3 or SEP 12.1 RU2
Your windows machines should have all the latest windows updates /Patches.
Apply application and device control policies, block USB etc.
Disable Autorun. From SEP 12.1 Autorun is disabed by default.
Please follow best practice guide to handle virus issue.
www.symantec.com/business/support/index?page=content&id=TECH105236
If Symantec is not able to detect then try to scan with available tools.
Symantec Power Eraser
http://www.symantec.com/theme.jsp?themeid=spe-user-guide
Symantec Endpoint Recovery Tool (SERT)
http://www.symantec.com/docs/TECH131732
If above suggested steps couldn't help then
I would also suggest you to run the Symantec Support Tool and submit the Suspicious files to the Symantec Security Response Team.
Using Symantec Support Tool, how do we Collect the Suspicious Files and Submit the same to Symantec Security Response Team.