I am so sad to report this, but I found multiple patterns as shown in the pictures, which are quite likely to be dirt or scars or combination of them, on the surface of the viewport on SR2 Chamber.
This viewport is for injecting/picking-off green laser for Y and picking off IR beam from SRC.

Last Monday, before vacuum work started, I attached a flange protection for this viewport and am sure there were no such pattern at that time. Today I removed it and found the patterns.
Even though the viewport was protected somehow, this happened. I suspect that so strong force was applied to the protection that the protection itself touched the surface of the viewport.
How can we protect them??? 

Editted at 21:30
Circled the patterns in the pictures