Geralt starts the game with one fire rune. Later, they can be purchased from the mysterious merchant, Haggard or Thorak in Vergen, or Falas, the Incredible Lockhart or Polycarp of Rinde during Chapter III.
To use a rune, Geralt simply drags it over to one of the rune slots on a suitable sword in the inventory panel.
Fire runes can also be used to craft red meteorite ore, though given that the price of a fire rune is much more than that of a piece of ore, it seems a poor use of the rune.