When i was used Symantec Endpoint Console 11.0.7. I was able to clear the still infected systems from Console.

But it is not be in SEP 12.1 so how to clean it?

You can full scan the system to clean the status.

The "Still Infected" number will go down automatically as the threat is completely removed from the network.

Cannot Delete the "Still Infected" Value From the Symantec Endpoint Protection Manager 12.1 Console

How to clear the "Still Infected" status from Reports in the Symantec Endpoint Protection Manager

##Edit##

https://www-secure.symantec.com/connect/forums/still-infected-status-report

https://www-secure.symantec.com/connect/forums/how-clear-still-infected-virus-logs-sepm-12-console-was-detected-dvd

that option is not available in SEP 12.1

if its showing the infection source as CD drive, put a CD and scan it

or 

run a full scan from Console, if the scan results are clean.. the status will be cleared automatically.

Hi,

You can not clean it manually in SEP 12.1 like in SEP 11.x version.

The "Still Infected" number will go down automatically as the threat is completely removed from the network.

This is a part of the enhanced management console.  The management server resets the Still Infected Status for a client computer once the computer is no longer infected. It gives a more accurate status for how many client computers really are infected.

SEP 11 is reaching End of Life on  5 January 2015. I would recommend you plan the upgrade.

Here more info listed about End of life:  

It doesn't work like 11.x anymore. With 12.1 it clears automatically once the system is determined to be clean.

Run a full scan and the system and make sure it comes back clean. SEPM will automatically clear it out.