One of the primary methods used to limit the size of a bonsai tree is pruning. Pruning is the careful remove of parts of the tree to shape it and limit the size. Properly pruning your bonsai is critical for the health and design of your tree.

The frequency and degree of pruning is heavily dependant on the size, age and type of tree being pruned. Deciduous saplings are not pruned at all the first year and are usually only pruned once the second year. With conifers it is best not to prune them at all until the third year.

If you are trying to increase the trunk thickness of a deciduous tree that is 3 to 5 years old you should cut it back twice a year. You should wait to do this cutting until the tree has grown to about 2/3rds of the planned final height. How many leaves you leave on the tree depends on the size and shape of crown that you are trying to develop. Usually you will leave from 1 to 8 leaves.

Mature trees that are more developed are usually not pruned until there are 5 to 8 leaves on the shoots. While the tree is growing the there is a hormone released from growing shoots that flows downward under the inner bark (bast) that prohibits buds from forming below. When you remove the growing shoot then the hormone production stops so the next bud down will start to develop. Since the development of this new bud starts producing the hormone again you will only get one new bud to start growing.

If a shoot has any leaves growing on it then the tips are usually removed in the late summer. This gives the shoot time to thicken and harden to survive over the winter and to develop new buds. The method used to remove these tips is called pinching and is normally done with tweezers or your finger tips. This will cause the tree to stop growing for the season and start preparing for winter. However, if the soil nitrates are high then the tree will probably continue growing instead of preparing for it's winter dormacy.

If you need to remove large branches from deciduous trees it is best done during the peak growing season. This peak season runs from early spring until mid summer. If you do the cutting during this time the cut area will heal much faster. When removing large branches you should use concave or wen cutters. These create a concave wound that will heal better with less scarring. You should always use a wound sealant to help protect the tree. Japanese paste works very well and is easily removed once the cut has healed.

With conifers you can safely remove large branches even during the winter as well as during the growing season. On a conifer you might want to consider leaving part of the branch intact on the tree. This can be turned in to a jin for cosmetic appeal.

Proper pruning is critical for the proper development of your tree. It allows you to control the size and appearance to create exactly the visual image that you want. Like many things proper pruning takes time and practice. Be patient and if in doubt about removing something then leave it. You can always cut it off later.