Use fresh seeds that have ripened within the past growing season, and germinate them in early spring so that the tree has time to grow and strengthen over the course of a normal growing cycle. Place the seed in a plastic bag containing a moist paper towel away from light for about a week or two to germinate.
Plant the seeds after sprouting into moist soil, about two inches deep in a small planting pot. Use a terra-cotta pot with a diameter suitable to the desired growth of your Bonsai tree. Place a plastic lining in the pot prior to adding the soil. This will help when you need to prune the roots to keep your bonsai tree small, and within your desired shape.
Prune the branches and roots of your bonsai tree after about a year of growth. The growth rate from seed to sapling fluctuates widely between species of tree. It may take many months before the sapling produces any branch growth. Keep the height of the tree trimmed to your desired size throughout the first year of growth. Wait for branches to sprout and produce leaves before trimming.
Trim branches throughout the growth of the tree just above budding nodes if you desire longer branches or offshoots. As offshoots grow longer, bend and bind the tree using garden twine or jute into your desired shape. Bind the branches loosely against a stronger branch or the trunk, and unbind after the branch takes to the new direction and shape. This will occur usually after a three or four months. Only cut about two inches or less at a time every other month.
Trim the roots as they begin to protrude from the soil near the bottom and sides of the pot's diameter, and keep them this way throughout the life of the tree. If you wish, let the tree grow larger in diameter, transplant it to a larger pot and allow the roots to grow to the diameter of the pot.