If you are talking about the long dark plastic window covers for the cabin, I removed both of mine ('88 28.5) last fall (along with the top hatches) to replace the plastic which was being crazed (showing small cracks throughout the plexiglass).
To remove the side windows, I used a heat gun to soften the glue that's underneath and a 1" scraper to work through the glue, be patient, lifting it as I went... I'm sure you will find that the back side where it attaches to the fiberglass, is completely covered with glue.
I ended up breaking both pieces to different extents, but I took heavy blue masking tape to get the piece to a complete original size, and then I used that as a pattern to cut new ones out, including drilling out the holes. I think you will find both sides are exactly the same size.
I purchased new plexiglass from Tap Plastics and used black RTV to reattach the windows, along with the screws.
One other note, in watching some YouTube videos from the manufacturer, I ended up using a torch in order to smooth out the saw blade lines that were on the edges. This looked very nice when I was done, but I have noticed that all the edges that I use the torch on are now crazed again. I'd suggest sanding the edged (but staying off the smoother surfaces).
Mike