I used to have this problem when I had my semi-feral cat Cirrus. He wouldn't let you even pick him up. The only way to get him into a carrier was to put it near the toilet in the bathroom and then I had to chase him with a broom into the carrier and then quickly latch it shut. It became so stressfeul for both of us that I had to stop taking him to the vet.

Now I only use the soft carriers which you can then flatten out to store them away. They all have zippers on the top of them so you can also just open it that way to put the cat in it. I usually don't have a problem putting any of my cats in the carriers. I've learned to close both bedroom doors so they can't hide under the beds though. I do have to chase some of my cats around for a bit. Scruffing their necks will help to keep them still while you put them into a carrier. Feliway will also probably help like Moosmom said earlier. Maybe you could start feeding him in a carrier and see how this goes. Good luck.