Endpoint Protection

there is a virus which symantec is not detecting but I know the filename and location of the file which is same on all infected computers.
Now I want to quarentine that file which i can do by adding the file to quarentine manually on the client but can i create a policy on my sepm console so that all clients will quarentine that file at once so that the virus can't damage our network any more.

That cannot be done...Quarantine files can be only manually added locally.
From blocking it centrally you will have to use APP & Dev Control or Firewall.

can i block a file to enter a system or from being created in a system if I know the md5 hash of that file ?

 If you block the application using firewall it wont be able to connect to any IP.
If you block it using App control it will be blocked as it will try to load into memory to do any type of action.