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Realize that rabbits are a prey species. Read your rabbit's subtle signals. Avoid picking up your rabbit, unless she likes it. Respect if your rabbit doesn't want to be handled.
You can think of a rabbit as a 'listener' rather than a 'talker' because their lives are tuned to being on alert for danger. They use a highly developed sense of smell (hence the constant nose twitching), hearing (those wonderful long ears), and prominent eyes to watch for threats. This means it is even more important that you understand your rabbit, so you know what she does and doesn't like. This can minimize her stress. Nature intended rabbits to live underground in tunnels during the day, emerging at dusk and dawn (when it's more difficult for predator's eyes to spot them) to graze on grass and plants. Because they spend the majority of their time in the dark, rabbits make limited use of visual signals, such as nuanced facial expressions or body language. Being picked up by a human can be a terrifying experience to some pet rabbits who go into a catatonic state, where the rabbit lies absolutely still, eyes open and staring, and does a good impression of being dead. Rabbits are ground dwelling animals. In the wild, the only time they leave the ground is when they're picked up by a predator. If that's the case, she will either scrabble, wriggle, and fight so hard you get scratched, or she will go completely still. Far from indicating she appreciates being cuddled, a rabbit that keeps deathly still in your arms is actually pretending to be dead in order to make the predator (you!) give her up as a bad meal and put her back down.  If your rabbit reacts in this way to being picked up, sit on the ground and encourage her to sit on your lap. This way her paws are in contact with a horizontal surface and she can learn to associate you with safety, rather than an instinctively alien and scary experience. If it's essential to pick the rabbit up, place a towel over her eyes, and use the rest of the towel to scoop her up. The darkness will help calm her.