Nice one.
You can use toothpaste to remove the paint from the canopy, which will also polish it. A car body colour restorer, such as 'T Cut' can also be used, being more 'aggressive'. I use the latter for removing scratches, and to give a smooth, clear finish.
Pics below show it being used to polish out the remains of where a frame had been on a 1/32nd scale Beaufighter canopy, frames removed then polished smooth.
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