You can shoo them into the box and then take them out when they are on your lap.
However, guinea pigs are scared by nature, so two giant hands coming to pick them up is pretty freaky at first. For me, I've had my guinea pigs for like 6 months now and they are just beginning to get over it...some of them anyway. Some guinea pigs are just scaredy-cats (one of mine is) and you'll always have to use the shoe box or put up with the frantic running. The long slow process is getting them to eat from your hand, then letting you pet them while they eat from your hand, then slowly progressing towards picking them up calmly. One thing that helps (A LOT-I MEAN IT) is when you're lowering them back into the cage, the second they start squirming, you stop, and hold them above the cage (keep a good grip lol) and wait til they stop squirming, then lower, if they squirm again, stop, and keep repeating until they are standing on the floor of their cage (while you're holding them) and not squirming.
If you do that every time you put them back they pick up on it really well. It really helps calm them in general bc they see that panic and squirming gets them nowhere. Literally