Stomping of the feet is a warning signal to the rest of the warren - it is usually used when the rabbit feels threatened or scared in some way. Occasionally they'll use it when really annoyed but usually its a threat.
The way to stop them doing it is simply to make them feel safe and secure. Make sure that the run is sheltered from the elements and that they have a couple of hiding places like a tunnel and a hide - rabbits always need somewhere that they feel they can escape to if danger comes along and as prey animals they can feel really vulnerable and nervous if they don't know the 'escape route'.
Animals like dogs, cats, birds, foxes and strange rabbits can also set them off, so try to keep other animals away from them. Children as well can be seen as a threat due to their quick movements and loud noises.
If they are not used to the run or being outside that can also make them feel insecure. So yeah, basically you need to find what is making them nervous and then once you fix it the stomping should stop. Or if it's due to annoyance you can fix whatever it is that they don't like- my Annabella stomps as she runs away after I've picked her up and groomed her, because it upsets her.