Care should be taken when handling your pet rabbit due to a very delicate spine. Never pick up your rabbit by the ears alone. Even though you may have seen cartoons or pictures depicting rabbits being picked up by the ears, for instance pulled out of a magician's hat by its ears, this is wrong and lifting your rabbit this way will hurt it.
How to start handling your pet rabbit
If your rabbit hasn't been handled much, thumping may mean they are frightened. In this case, it's best to not try to pick up your rabbit until you've worked with your rabbit a bit more and gained their trust. Try getting down on the floor and just getting close to your rabbit without grabbing for them. Rabbits are naturally curious, so if you are sitting quietly on the floor, not paying much attention to them, eventually they will come over to check you out. When they do, continue to sit quietly, don't make any sudden movements or reach out to them. They'll soon learn that you are safe to be around.
Depending on the rabbit it may take some patience to wait until they are ready to approach you. Without too much effort you can make a habit of letting your rabbit out and sitting on the floor in the evenings while you watch TV, read a book or listen to music. It provides a nice routine for your rabbit, gives her a chance to stretch her legs and explore a larger environment than just her cage. Plus if you are doing something else rather than just waiting for your rabbit to approach the time will go quickly for you instead of stretching your patience.
After your rabbit becomes comfortable being near you, you can start petting them, or scratching around and between their ears. Keep petting sessions short at first, move slowly, and don't restrain your rabbit if he wants to move away. As he comes to trust you, your rabbit will let you pet him for longer periods of time and eventually you will be able to pick him up. Start with lifting him onto your lap while you pet him. Before long you may find your rabbit coming over to jump onto your lap for some affection.
How to pick up your rabbit
Once your rabbit is used to physical contact with you it's time to start picking her up. Your rabbit may feel confined at first when you pick her up, so keep the sessions short, lift her and hold for a few seconds before putting her back down again. This way she'll learn that being picked up is no big deal. If you try to hold her against her will when she's trying to wriggle out of your grasp, it makes for a bad experience for her that will only make it more difficult for you the next time.
There are two methods for picking up a rabbit.
Generally the easiest method to start with is to pick your rabbit up and keep him cradled against your body with one hand or arm underneath, supporting the weight of your rabbit and the other arm around the outside, the side of the rabbit that's away from your body. Make sure that your rabbit's feet are resting on your arm or hand, especially the back feet. The rabbit is likely to feel insecure and struggle if their feet are dangling without support. This method is usually the easiest for beginners but also allows an easy progression from petting the rabbit on your lap to cradling it in your arms, to standing and holding it as described.
In the second method for picking up a rabbit you want to start with stroking your rabbit around it's neck. With one hand, grasp the rabbit by the scruff and slip the other hand under his back legs. The hand under the back legs should be supporting the full weight of the rabbit, the scruff is more for balance and stability. You want to keep the rabbit in a position similar to it's natural sitting position, with the head higher than than the body. You then carry your rabbit in front of you, either resting against your body or a comfortable distance away. Below is a video that demonstrates how to handle your pet rabbit.
So there you have it. The key to working with your rabbit is to be sensitive to it's needs. If it's afraid of you to begin with, give it time to be around you and learn to trust you and build up contact gradually in a way that doesn't stress your rabbit, and you'll will be able to pet and handle even the most timid rabbit.
These are just some of the basics of rabbit care. For a more detailed treatment of the subject, visit How To Train & Care For Your Rabbit.