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So here's whats happening. I marked all of my faces as freestyle. If I press 'clear freestyle face' the annoying green line over everything stays. Is there something I'm doing wrong or is it something different to freestyle?
It seems to me you marked freestyle edges, not faces. The green lines are the edge marks.
To clear the marks go to Edit Mode, press A to select everything, then Ctrl+E to bring up the Edges menu and select Clear Freestyle Edge.
Clear Freestyle Edge
Required, but never shown