Most of the time, there's no need to do anything. The hole through the tire is mall, and the inflated tread is under compression, which forces the hole closed. If the hole is bigger, the tire is toast, and it needs to be replaced. What's big enough to ruin a tire depends on the tire. Fat tires, treaded mountain bike tires, and heavy flat resistant tires are more tolerant of holes than light weight racing tires.

That's a 3" long #10 decking screw, which poked three or four holes in the tube before I stopped. I know where that was, because I marked the tire, but I couldn't find the hole when I went looking for it. I know from experience that a smaller screw ruins a lightweight 28 mm tire.