I have a 5/8" thick x 4' x 7' glass table I surface the manifold on. Use painters or body masking tape to tape 400 grit carborundum paper to the glass and use some kind of oil on the paper. If you don't have any thin oil you can use olive oil. YES olive oil.
Put it in the middle of your paper and hold the flange flat and work in a figure 8 cleaning the flange form time to time. You will notice that there is rubber on the flange that comes off first then there is a finish like varnish that will come off next. There will be dark area that show up with the varnish still on them those are the low spots. Keep cleaning and do the figure 8 until all spots are gone and the flange is shinny. Shine a light from under the glass and see if you can see any gaps between the glass and the flange if you can't your good to go.