One controls the shape and growth of the bonsai by pruning limbs and foliage that fall outside of the overall design. While this is done by removing new growth, it is important not to remove all at once as this will affect the health of the tree. Pruning will achieve three main results: One, it can be used to direct growth; if one side of the tree is pruned heavily and the other side less, the growth will move toward the less pruned side. Two, it will ensure the tree continues to grow in the intended design. Lastly, pruning is one of the main ways to make a tree appear to be a miniature full-sized tree of great age.
The first thing to consider when pruning is the type of tree being dealt with. Some trees may be pruned any time of year, some only during certain seasons. It is important to research a particular tree, perhaps by seeking the advise of an expert at an nursery, to find the best time to prune. A good thing to keep in mind is that whatever is appropriate for the full sized tree is also applicable to its bonsai counterpart. It is then necessary to leave enough time for the plant to recover from the pruning. Once a proper schedule of pruning is established, the tree will continue to grow and be healthy for many years.
Pruning may be used to strengthen the trunk in areas that are weak. If extra branches are left where the trunk needs to be strengthened, it will promote growth in that area. In fact, concentrating the pruning to the trunk will give the tree the signature bonsai qualities of imaginary age and size. "Difficult" branches that cross the trunk or each other should be removed, as well as those that grow back towards the trunk or generally take away from the desired shape of the tree. Branches that stick straight out of the trunk toward the viewer are known as ‘eye-pokers’ and should also be removed.
Another important rule to remember when pruning is ‘as above, so below.’ Whatever pruning that is done to the branches and foliage of the plants must be matched by pruning of the roots. With the plant removed from the pot, comb out the dirt near the end of the roots. While it is possible with many species to prune the buds on top of the plant by ‘finger pinching,’ the roots should be cut cleanly with sharp scissors. It is possible to leave more root growth below the ground then foliage above, but be sure not to leave too much. A plan with full roots and heavily pruned branches and foliage will likely have a ‘growth spurt’ to make up for the pruning.