How to fix a bad KF flange? 
Here is an interesting question for those who are familiar with vacuum science techniques. In the attached picture we have a damaged surface of a KF flange, which comes from the turbo pump outlet and connects to a roughing pump. We believe this is a source of major leak (our roughing pump or helium leak-checker can pump out a small 4-way cross efficiently, but the same 4-way cross attached to the turbo pump (inlet sealed) cannot be pumped down efficiently).
How would one fix a scratched flange surface like this? Tried putting some silicone vacuum grease but didn't fix the problem.
UPDATE (01/31/2019) : We tried the PTFE o-ring as suggested below, but it did not prevent the leak. My suspicion is that because the damage is on the inner diameter of the flange, the o-ring cannot simply fill in the gap resulting in the inner diameter (only the centering ring, not the o-ring, touches there I think).
UPDATE 2 (03/08/2019) : The turbopump was repaired by Duniway Stockroom. What they tell me is that the scratches were not to blame for the leak! What matters for the foreline flange is the presence of deep scratches that may connect to the outside, and in our case, no scratches were of this kind. The deep scratches that we had were closer toward the inner diameter. The actual culprit for the leak was that there was a crack in the joint between the foreline flange and the main body of the pump.
 A: I can think of three possible fixes:
1) The easiest "work-around" involves using a teflon gasket.  Teflon is known to cold flow and conform to the shape that it is clamped between.  With sufficient compression, such a gasket should fill in the gaps that obviously exist in your present flange face.  Assuming that this works, you will probably want to keep quite a few teflon gaskets on hand, as each time you compress the gasket, the teflon would get squeezed to thinner and thinner dimensions.
2) Have a good machinist resurface the current flange face.
3) Cut off the existing flange and weld a new one on.  This is probably not an option, or you would have done it already.
A: I have fixed flanges like this by sanding. If your flange is aluminum, this won't be too hard; if it's stainless, it might be fairly tedious and painful! 
Start with a coarse-grit sandpaper, around P120-P200, and sand out the visible dents and scratches. Then work your way through a couple of intermediate grits up to at least P600. Sand in a circular motion around the flange to avoid making scratches that cross the o-ring. Make sure to moisten the sandpaper (I usually use isopropanol) to keep the dust down and to plug the exhaust tube and clean its outlet regularly while you work, as you don't want any of the grit to migrate into your turbo. 
As a side note, I've found Apiezon L to be a very good low-outgassing grease for ultra-high vacuum, but it's always better to fix leaks if you can rather than greasing and hoping for the best. 
A: Use a soft metal, thin, non flexible but moldable gasket like lead. Simple.
