Some snakes can't be 'herded'. And especially if it's after they ate, they're in their warm hide, digesting and not wanting to be bothered; poking and prodding trying to get them into a box probably increases chances of a regurge. Sometimes you can't clean around them either. Some snakes (like mine), when they poop, they also soak the entire cage with piss..so you have to handle up.
I'm a little paranoid and don't want my baby sitting in his own waste, so I just scoop him up quickly, sit him in my bed and throw the cover ontop of him (so he doesn't have to move around looking for a place to hide) and clean as fast as I can.