Auto-protect will scan a file , by default, would run when a file is accessed or modified (scans the files when they are written, opened, moved, copied, or run)..I think this is maximum possible in your case.Other wise as Pete told if this is happening at a particular time you can schedule a scan
Does Symantec Endpoint Protection or Symantec Antivirus Scan USB flash drives?
Currently there is no other option with this product...
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There is a command line scanner is present in SEP namely doscan.exe.But now it is do not having the capability of scanning individual file or folder.There is an enhancement request for it.
How to run a scan from a command line using Symantec Endpoint Protection using DoScan.exe
Doscan.exe enhancement required