In math, when you subtract, you take one number away from another. If you subtract four from ten, you're left with six. You can also use subtract to mean "take away" in a more general sense, as in "If you subtract some of the salt from the recipe, the pasta will be healthier."
When you're doing math, you know you're supposed to subtract if you see a minus sign. Subtracting gives you the difference between numbers, and you can see this in a real way when you subtract actual objects instead of numbers. If you have a dozen cupcakes and subtract ten of them, you have only two cupcakes left. The Latin root of subtract is subtrahere, "take away or draw off."