Procedure can vary depending on vehicle, but a common tool is a pipe knife, which is just a long handled utility blade holder. Another is some form of an osculating multimaster type tool with a thin flat blade such as Fein. Cutting wire is another. As long as you cut it loose without damaging glass or vehicle, that's all that really matters.
Most modern glass uses black urethane for adhesive sealant. You can use the standard caulk gun sized tubes of 3-m stuff from automotive chain stores, which ones I've seen are overpriced at 20 something a 10oz tube. Urethane has a short shelf life & gets stiff near or after expiration date. Most professionals now use a fast drying urethane from a large sausage gun sized tube, which is stiff when in date & takes a battery or pneumatic gun to pump it.
Some glass has a type of rubber molding you need a new section of , some doesn't.