Warp Flute 1: In world one, level three, go near the end of the level until you see a white block. Step onto this white block and duck, and after a while you will fall behind it. Stay behind the backround while going all the way to the end of the level.
Warp Flute 2: In world one's fortress, go to the area where the ceiling is open (it is just before a door with a skeleton koopa). Make sure you have a raccoon leaf. Fly up above the screen and then move to the end at the right. There should be a hidden doorway.
Warp Flute 3: In world two, go to the top right corner of the map. Use a hammer to break a boulder up there, and then continue to the right to find a hammer brother. Beat him to get the flute.