To anneal copper you just heat it to dull red and let it cool or quench
it. The rate of cooling makes no difference. The only way to harden
copper is to work harden it.

So I would anneal the whole length of pipe.
You don't have to get it all red hot at the same time. Just start at
one end and get that red hot and work your way down the pipe. As you
square it, the copper will be work hardend. But only the part that you
have done something to work harden it.

Using a mallet works, but the square copper tubing shows that it was
hand done. It does not have factory looking flatness. Could be a good
thing or a bad thing. Depends on the look you are trying to achieve.

Stop by Home Depot, Lowes or wherever and get a ten foot length of 3/4
copper pipe and try a couple of experiments. Copper pipe is not too
expensive.

Dan