I don't use a net or take the fish out. I start on one end with a collection bucket, with the fish at the other end. Then, When half of the gravel is gone, I 'chase' or 'guide' the fish towards the end which now has no gravel, and I am free to get rid of the gravel at the other end.
To be clear, I very rarely remove all gravel, I usually remove some gravel to seed a new gravel bed or filter with the necessary beneficial bacteria.