Make sure the vac-formed part is held steady and, with a new blade in the scalpel, very carefully start to score around the base of the canopy. DO NOT try to cut through the part, as this can cause a split or tear. Keep gently scoring, until the part is separated. This can take some time, maybe an hour, so, if needed, take a break. Don't rush, be patient, and it'll come free.
Once it's off, then marry it up to the cockpit, to check fit, and then gently sand around the edges as required, checking fit regularly.