Hi Fullmoon,
If I understand you correctly, you will want to define a webfilter profile for a policy that is attached to all of your branch sites and push the policy out. This would ensure you are uniform.
If for some reason you mean being able to send out a webfilter without it being part of FortiManager policy, it' s possible but not recommended because any future pushes from FortiManager would wipe it out.
So first, let' s start with the recommendation that you upgrade to the latest FMGR patch.
If you have a special need to bypass FMGR policy, you can enable scripting by going to System -> Admin -> Admin Settings. Go back to Device tab -> Script and then create new CLI Script. Enter in the CLI commands for the webfilter profile just as you would if you were on a FortiGate. Then override the target to run directly on the device (CLI). You can run the script against the relevant firewalls and it will send those commands out, but this is not a sustainable way to do it.
So please use FMGR policy to do this if at all possible. Hope that helps.
Cheers!
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Sean Toomey, CISSP FCNSP
Consulting Security Engineer (CSE)
FORTINET— High Performance Network Security