I have a hen sitting on 6 eggs, so far I have left her alone except for the odd check in the box but I decided to candle the eggs and they are all clear My question is how long do I let her sit on them and how do I go about removing them, can I just take them and see if she will go again or will she eventually reject them herself?????

Take them all out and throw them away. At least it gives her a chance to get it right a second time and not waste time sitting on dud eggs

Clear eggs mean they haven't been fertilised. You can usually tell if they are fertile or not by day 4 of when she started incubating.

Remove them and let her do it again. Remember to clip both birds fuffy butts and don't cut the 2 little feeler feathers on the vent.

The one question that wasn't asked was how long ago did she lay them? The first few may not be fertile but if she only laid any of the others with in that last five days you don't know for sure if they are fertile or not. I would not throw any of them away until each egg is at least five days old... then if they are still clear I would remove them as soon as possible. You don't want her sitting in a next isolated and not "exercising" for there to be no out come. As KAZ said it gives her time to get a second chance. Good luck let us know how you make out.