Are you implying that helium weighs nothing? That it's unaffected by gravity? What's actually going on is helium is lighter than air, so the pressure of the air around it pushes it up. Just because it rises at ground level does not mean it weighs nothing. I can jump, but when my feet are off the ground it does not mean gravity has stopped pulling me down, it just means I have moved upwards with enough force to overcome the effects of gravity. Eventually my upward momentum will slow enough for gravity to pull me back down. Same thing with helium, eventually it gets high enough that the neutral air molecules are sparse enough that it can float on top. It doesn't continue to rise past that point because gravity is still pulling it down.
So what is the weight (that is, what is the force of gravity pulling down the helium molecules without ambient air pushing it up) of helium? If you have a cylinder of a known weight, you can fill it with helium and subtract the weight of the cylinder. What's left is the weight of the helium. To measure this effect without air pressure pushing the helium up, you might need to do this in a vacuum, but the logic is there and I think my analogy fits. I weigh the chicken on a plate and subtract the plate to find the weight of the chicken.
What I was asking is "how do you weigh a gas without it spreading around and mixing with the air?" "Putting it in a cylinder" is the answer I was looking for.