The only problem you may see (assuming the plastic is completely clean, clear & unscratched) is a circular pattern of light and dark bands in small patches, called Newtonâ€™s rings http://en.wikipedia.org/wiki/Newton%27s_rings
but youâ€™ll only get them if the plastic (or plain glass) is in contact with the film.
Anti-Newton glass has a very fine texture, usually on one side only, giving it a slightly diffuse appearance. You should be able to buy a small sheet from a specialist supplier, such as Better Scanning http://www.betterscanning.com/scanning/insert35.html
... to be placed on the lightsource side of the film as Costas says