Leopard geckos are prey animals. That is, one of their main purposes in life in the wild is to provide food. Of course, they are'nt that keen on it. 
Whenever your hand comes in from above, it casts a shadow on the ground, and your gecko's mind screms "PREDITOR!" and, of course, he would run, since leos have a stronger flight than fight instinct. If they have no place to run to, (ie. you have them cornered or have taken away their hides) they will hiss and probably try to bite you. They're trying to look dangerous, so that way your "killer hand" wont mess with them.
How do you prevent unneeded fear and stress, yet still handle them? easy. First, try to incorperate your hand with a good thing (food) whenever you feed him, make sure your hand goes in the cage. I dont know how good a leo's sence of smell is, but I also like to rub my finger around the rim of a mealworm bowl (if you feed them mealworms, if not the water bowl) so that way, he is around your scent while he eats. Next, after he has settled into his new home for a bit longer, turn the lights out and make it night. He should come out. before he heads out of his shelter, however, make sure your hand is in the cage. keep it perfectly motionless. For a few weeks do this. dont expect him to go bounding up to your hand like a dog, but after a while, he will learn your hand is not a threat. eventually, he will get curious, or will totally forget about it, and step up onto your hand. For the first few times, even though it is exciteing, keep your hand still. Just let him crawl over it. After a while, slowly life it a few inches off the ground.he will probably jump off, but dont worry. The next night, go a little tiny bit higher. dont go any higher than his body length untill he will stay in one place on your hand. Eventually, you will be able to lift him right out of his cage. Just remember to be slow and predictable, and not make any sudden movements. even putting your hand into the cage at normal speed will send most off running.
Remember, always lift from under the belly- dont have your hand come from overtop like a hawk. Make sure his feet always have somewhere to touch, they tend to panic when they feel air under them.
Good luck, and happy herping.