Wriggles and shakes himself frantically, then kicks his feet vigorously as he runs away. Even the vet (not his usual one) couldn't handle him to check his wound when I picked him up after neuter. That's how bad he is.
I have a few like this. The feet flicking is digust, but, having seen complete terror at being handled, its not the same. If he was scared, I would expect him to leg it, or to slink away, no feet flicking. Which implies he just doesn't like it, as opposed to being scared of it.
We all have to deal with things in life we don't like, including rabbits (vaccinations, operations, nail clipping, medications, etc), for their own benefit.
Approach him low, and slowly. Slip a hand over his eyes, and then scoop him up from there. Once you have him he will likely flail, so I have one hand over their eyes and the other under the front end (two fingers in between his front paws), and, making sure I'm sitting down, support his back end with my stomach/thighs and where I 'bend' to sit (how weird does that make me sound), i.e. so bunny is facing outwards. When they are calm, and I am calm, I then try to do whatever I'm trying to, but if they wriggle, they go back to this position.
Sometimes it can also work (provided they are not a biter), holding their bum in one hand, having them facing sideways across you, and having their head under the crook of the arm that is holding their bum- you then have a free hand to help steady him and do whatever needs to be done.
I would suggest ensuring his eyes are covered.