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I don't like holding them by the scruff of their neck either but sometimes it's the best way to get them to submit to being picked up. You have to grip quite a lot of skin so they're held very securely. They should calm down immediately, just like a kitten does when it's mom picks it up by the back of it's neck. If I think the rabbit is going to be nervous, or say if a dog comes running up, I will lay my hand on the back of their neck just in case. That way, if they do react, I'm ready. You can usually tell ahead of time because they'll tense up.