When I am doing Gold sputter coating on my PDMS sample (have some micro-structures) for further SEM investigation, I found some type of structure damage on the surface.
PDMS can be tricky to image with EM. Could you post an image of a damaged sample? It will be easier to make recommendations if we can see the specific type of damage you are experiencing.
I have no idea about PDMS, but there are some materials whose surface features does not survive sputter coating. The best way to observe these specimens - without any coating, at low accelerating voltages, 0.5-1.5 kV.
Example. Pictures of coated and not coated specimen: