Monkey, well, it depends on the bunny on whether you need to get them adjusted to it or if it's better to leave them alone. My two, if I pick them up often, will RUN from me and REFUSE to be picked up anymore, freak out when I do pick them up and generally make it horrid and difficult, in an emergency they would be in trouble. However, if I leave them ALONE and only pick them up when needed, I can reach down and snatch em no problem at all, no running and no fighting me. When I had to medicate them, it caused the freak out run response cause each day I had to pick them up and they knew it was coming and for two weeks after medication ended, they still ran from me whenever they saw me, thinking they were going to be picked up. When I nail clip, I have two very calm bunnies since I only pick them up when I need to. And for vet visits they are calm until the vet goes to try to pick them up since they hate strangers. lol Other bunnies do better when they get used to it though.
But since your bunny OP is already freaking out about being picked up, I would say when you DO pick him up try to make the end result a pleasant experience, hold securely (I hold mine against my chest, with one arm supporting their back legs/back and one supporting their shoulder blades since it makes them fight less) and always treat afterwards. I find treats are a great way to make any bunny like something more. Craisins work well for my two. When I pick them up, I do it in one quick motion, rather than slowly, since they freak if they are in the air and not supported by my body. So it depends what your bunny prefers. Mine get a little pressure on the shoulders, then two hand pickup (being sure to support the back/backlegs) directly against my chest while I am stooped down, in one fluid motion. This causes them to not kick, fight, struggle or attempt to jump away once they are supported. If I try to go slowly, they kick and flail and try to do the bunny flip arounds that are so dangerous to their spines. I also find positioning it so they can hear my heart beat and remaining perfectly calm myself helps a ton to keep them calm.
Again, what works best depends on your bun. For Powder petting him keeps him calm enough to pick up and for Stickers it has to be a quick snatch-n-grab cause she's not the pet type, she's the "leave me alone or I shall foot flick you" type.
Experiment with safe, secure pick up procedures and find the one your bun accepts the best. Just be sure to be aware if they struggle too much, let them go. Bunnies can hurt themselves in their panic to get away from their owner, so you want to find that method that keeps the flailing to a minimum.