If you direct the photons against the motion of the atoms, the atoms will slow down. It's like throwing ping-pong balls at an oncoming bowling ball. If you throw enough ping-pong balls, you can stop the bowling ball. This process works like the cooling of a cup of coffee. The hottest molecules escape, which leaves the rest with less energy.
Scientists trap a gas of atoms and use magnets to remove the hottest atoms.
Aaron, thanks for your question. And with thanks to the National Science Foundation, we're Block and Byrd for Earth and Sky.