Usually you sacrifice the panels themselves. So, for something like a wing gun bay, you drill holes around the INSIDE edge of the panel and then "connect the dots" by cutting through the plastic between the holes. Then trim the opening to shape slowly, working outward toward the edge of the panel. You can use files or sanding sticks to keep everything true. New panels can be cut from thin plastic sheet. If you are using an aftermarket detail set, they should provide new panels. Note that real aircraft skin is very thin, but a kit wing or fuselage is mega thick. So, you will want to thin it out from the inside, too. Internal structure can be made from plastic sheet, rod etc.
I do 95% of my modeling work using a hand twist drill/pin vice with an assortment of bits, a couple of X-Acto knives, sanding sticks and a good quality sprue cutter.