Why plexi polish? I would think a commerical Vinegar based glass cleaner
or even Vodka would work as well or better.

It is after all glass and not plexi, the cloth you use is probably more
important, I would use soft cotton "Non lint producing" rather than
any paper or paper towel product. You could probably use lens cleaner
fluid for that matter.

Bon Ami. Clean hands only. It has a talc like grit
and should be safe. Bon Ami, since 1886. Dan

  Have a look at the surface using a magnifier and a light
source you can shine at various angles. See if its scratched
or if the marks are just on the surface. Its also possible
the glass has been coated with something, perhaps to
eliminate Newton's rings.
  If its something on the surface, and you are sure its not
a coating try any of the "streak-free" glass cleaners first.
If this doesn't work, try 99% Isopropyl alcohol (available
at many drugstores). If that doesn't work try Acetone.
Acetone is a standard cleaner in optical assembly. Some
petrolium based materials may come off with Naptha. Naptha
is available as lighter fluid, like Ronsonol.
  If the surface is scratched you may not be able to polish
it out with any readily available material. Bon Ami won't do
it. Its possible the Plexiglas polish might work but
Plexiglas is much softer than glass plus it flows a little
when polishing tending to help fill in cracks. The problem
is that any abrasive capable of removing the scratches will
also turn the holder into ground glass.
  As a last resort you may be able to get optical glass
flats from Edmund Optical or some similar company. Optical
glass is clear when viewed sideways. If the holder is green
when so viewed thin window glass will do the trick at a much
lower price.

Be careful with this. The glass maybe AntiNewton and thus the finish
you have maybe be deliberate.

Bob  AZ