You can make a flute one of two ways either by creating an oval shaped hole at one end, aligned with the other holes, so as to be played in a sideways fashion, called transverse. If you wish to have an end blown flute, played in front, make a tapered mouth piece with a notch approximately far enough down the flute so as to be visible looking down the nose with one's lips on the mouth piece. The finger holes should feel comfortable in your grip and can range from 5 to 9 in number and a optional thumb hole for register variation.
The question asked was how do you make a flute? The first thing you must decide is what material you would like to make your flute out of. A bamboo flute can be made out of an old bamboo fishing rod or a plastic one can be made out of PVC piping. You can find more information here: how do you make a flute