Had a similar experience a few days ago. What worked for me was to go to the autoparts store and get some 1500 wet/dry and some Turtle Wax polishing compound. Using soapy water I sanded the canopy till smooth. Then I used the polish. Took a while but no marks are to be seen.

In researching this problem I came across an article that had an alternative solution. Sand smooth and paint with clear hobby poxy. I do suggest if you want to try this to first test on a scrap.

Safe Flying!