Winter is a great time to prune most woody trees and shrubs because most plants are dormant or not growing very actively. You can remove poorly placed branches so that when the plants start growing in spring their energy will be put into the remaining better branches.
Deciduous trees and shrubs that drop their leaves in the fall are easier to prune now because, without leaves, you can readily see the structure of plants.
Here is a quick guide for what to prune or not to prune now:
Prune any time of the year: Dead or broken branches on any plant, but be sure they are really dead first. Dormant branches can look dead. Scrape the bark on a twig and look for the green layer under the bark. The green means it’s alive and those buds will sprout out with new leaves come spring.
You may also notice that live branches have more prominent buds than dead ones, but this may take some practice to recognize.
Prune now: Deciduous shade trees and plants that bloom in the summer (Butterfly Bush, Chaste Tree) are best pruned now. Vigorous blooming plants like roses and deciduous fruit trees (especially pear and apple) are best pruned in winter to clear out weak twigs and encourage good structure for blooming and fruiting. This is a good time to prune citrus if their fruit has already been harvested and they have not yet bloomed.
Careful: Plants that you grow for early spring flowers, such as azaleas, dogwoods, camellia and lilacs, already have set their flower buds and too vigorous pruning may rob you of their spring bloom. Light pruning is fine at this time, but wait until after they bloom for major restructuring.
Wait: For frost damaged plants like citrus or Queen Palm, wait until new growth appears in the spring and remove any frost-killed parts. Do not prune apricots during the rainy season because they are susceptible to a fungal disease which can damage or kill them. Prune them only during the summer so rain does not spread the fungus into the pruning cuts.
Remember, do not use “pruning sealer” on pruning cuts. University studies show that it actually causes more decay than untreated cuts.
Here are some great sources of information on how to prune specific plants:
University of Florida has excellent guide to pruning many kinds of trees and shrubs.
Cornell University has a very useful guide to planting and maintaining trees and shrubs.
Information from UC Davis on pruning and train fruit trees provides extensive information for home fruit growers. Different fruit types require different pruning. They also have pest management information.
The American Rose Society website will help you prune your roses to encourage blooms.