Hello,

To Run a Scan as System, You can schedule a single scan with Doscan.exe using one of the following methods:

• Using the Task Scheduler interface
• Using the Scheduler Service and AT commands

Using Task Scheduler 

The following steps show how to schedule a scan by using Task Scheduler on a computer that runs Windows 2003/XP/2000 and Symantec Endpoint Protection client.

To schedule a scan

1. In the Windows Control Panel, double-click Scheduled Tasks.
2. In the Scheduled Tasks window, double-click Add Scheduled Task.
3. In the Scheduled Task Wizard window, click Next.
4. Click Browse.
5. In the Select Program to Schedule window, find the folder where you saved the Doscan.exe file.
6. In the Scheduled Task Wizard window, click Next.
7. Type a name for the scheduled task, set the frequency, and then click Next.
8. If you selected anything except "When I log on" or "When my computer starts", set the time for the scan to begin and click Next.
9. Type the credentials for the user account under which the task should start and click Next.
10. Check Open advanced properties for this task when I click Finish.
11. Click Finish.
12. On the Task tab, click the Run As field.
13. Press the End key to move your cursor to the end of the line.
14. Press the Space bar and then type the drive letter of the drive that you want to scan at the end of the line.
15. Click Apply.
16. Click OK to close the task window.

You must perform these steps for each scan that you want to run. For example, if you want to run a scan at 12:00, 1:00, and 2:00, you must create a task for each scan.

Using the Scheduler Service and AT commands

You can use the AT command to schedule scans each day. The AT command is dependent on the scheduler server; therefore the command is only available when the Task Scheduler service is started. Here is an example of the AT command that you might use: 

AT \\<Computer name> <time> /every:m,t,w,th,f,sa,su "C:\Program Files\Symantec\Symantec Endpoint Protection\doscan.exe <drive>" /s

Notes:

• <Computer name> is the computer name.
• <time> 
  is expressed as hours:minutes in 24-hour notation (00:00 [midnight] through 23:59).
• <drive> is the drive to scan.
• The path to Doscan.exe in this example is the default path for an installation of Symantec Endpoint Protection and may not match your environment. Use the correct path when you schedule scans with the AT command.

Also check this Article:

How to create extended scheduled scans.

http://www.symantec.com/docs/TECH146668

Hope that helps!!