The OEM windshield seals on an FD are pressed into the gaps after the windscreens are glued down to the chassis. They bond to the glue and must be cut back out if you want to preserve them. The factory manual has detailed instructions as to how to cut them out. You will likely need the curved knives commonly used by installers.
Its rather easy to cut them out if you will just replace them with new seals. I used OEM seals that I ordered from Ray Crowe. They were not cheap. $100-$200. There are also a few clips you need if you want an OEM fit.
Cheaper aftermarket seals are probably available, but I much prefer the factory fit and finish.