Usually the clear stuff is silicone and is on the sides and front. On the roof will be a lap sealant if your roof is rubber. Silicone should not be used a rubber roof.
I used Krud Kutter silicone remover and it worked pretty well. I scraped off old silicone with razor blades (very carefully) and a variety of sharp wedges made from hardwood scraps, then used a toothbrush to apply the remover and let it sit for about half hour. More scraping and wiping with rags to get it all clean. I followed up with PolySeamseal caulk. I just like it better than other caulks. So far, I've removed, cleaned, and reinstalled about 100 feet of exterior trim with about 200' left to go. Wish the grandkids were old enough to teach to do it.
Good luck.