Lots of bees in the colonies I've been removing lately. Too many to see what I'm doing, so I vacuum enough bees to allow me to see what I'm doing.
If bees are mean vacuuming helps as numbers are vastly reduced.
If bees are relatively nice and you can see the comb sections, I like to just go in and work amongst them, gently placing my fingers and hands between them, around them, cutting and transferring comb sections with bees.
I often transfer comb sections full of bees, I try not to vacuum bees off comb sections I am transferring.
I always try to finish near dark/at dark/after dark to get 99.999999999999% of the bees.
If its a complicated one, starting early is a good idea. Remove and transfer, set box/boxes up and go eat lunch, catch a swarm, etc... Then come back and seal box and place in truck.
If you are left with a ton of bees in the void space, you may have missed a queen, if you know she has gone into a crevice come nightfall and she still hasn't come out, if you can, leave and come back later or next day and usually she will be out with the rest of the bees.