In order to mine Gems, you will need a Gem Scanner fitted to your ship so as to be able to locate them.
You will also need to have a planet that gems traces have been found on a soil sample.
You will need to fly at low altitude (<3000m) over the surface untill you get the message top of screen indicating a gem cluster has been detected.
Use the Radar to pinpoint the gem clusters and after getting withing distance, mine them in the same maner as you would asteroids.
Gem clusters do not grow bigger when left so they always will act like small new asteroids and therefore heat up and mine very quickly.
Yield will increase with bigger mining beam and with higher deep core mining skill level