When making any item in a crafting table, it renders the items on top of the table.
When crafting tools, weapons, armor, and other items that do not stack, you click the item in the output slot (like normal). Then it "kicks" you out of the crafting table so you can see the items on top. You then hit the top of the table three times to finish the crafting process.
For metal tools and items, there is an additional step. Instead of getting a normal, say, an Iron Sword, you get a Hot Iron Sword, which you must cool by either dropping it in water or right-clicking a cauldron of water.