The root of the Magic tree is obtained with the Farming skill. Level 75 farmers may plant a magic seed in a Tree patch, and once the tree has grown, the farmer may use an axe to chop the tree down to a stump. As with all player-grown trees, if you do not use a spade to dig up the roots, the tree will re-spawn and can be cut down again. The farmer may then use a spade on the stump to dig up the tree roots, clearing the patch for another tree, and putting the Magic root into the farmer's inventory.
As with all tree roots, the magic root may be used in a compost bin to make supercompost.