If you have not read the first Edition of Feral Cats - Handling 101, I encourage you to do so before reading this post. It may explain a bit.
Ok, so now you have Mr.Feral Cat in a crate instead of in the live animal trap. Now what? Well, now you will have to move him and get him situated in a holding location until you can get him in to the clinic for the good-ol Clip-N-Snip.
Here are a few pointers to keep in mind when working with this guy ...
First off, DO NOT stick your fingers in the cage and say what a cute kitty he is! He is NOT a cute kitty. He is a wild, savage feline who will not hesitate to take your arm off. Keep your limbs on this side of the bars and don't tempt him. This will keep him safe because the more you are close to him, the more stress you put on him. Stress is not good for his health and if you are going to be prepping him for surgery, you want minimal stress.
Secondly, DO NOT try to pick up or move the cage without covering it with a blanket or towel first. You'll scare the crap right out of him (yes, literally). If you have a true feral, he may have already expelled his anal glands at this point from the stress. TRUST ME ... stress is not good for these guys!! It smells. If you ever need to prove that stress is a tangible thing, go get a feral cat and hold him in your arms. You'll see and smell what stress really is. Not to mention that he can probably fit his paws through the bars and get your hands if he chooses to go on the offensive and you are trying to move the cage without the protection of a blanket.
Thirdly, DO NOT open the cage and try to put food/water/litter box in there with him still inside. If you did not think to put one in before putting him in then DON'T try to work around him. Again, trust me. What you do is you move him to another crate first (refer back to Handling 101 for specifics), then put litter box/food/water in and move him to the crate that has these things already fully furnished (unless he's going for surgery within 12 hours, then just put litter box with no food/water).