The spores of many rust fungi can overwinter on dead leaves or fallen branches. It is important to clean these up regularly to prevent further spread of the infection. If sanitation is not made a priority, other control methods are useless. Burn any infected material or place it in a garbage bag, tie it and place it in a garbage can bound for a landfill. Composting infected material is not generally advised since it isn't guaranteed that temperatures in the compost pile will get high enough to kill the fungus.
Rust fungus on the bark of smaller branches and twigs can be pruned out. Cut below the rust into healthy wood. Use sharp shears or a sharp saw as jagged edges on cuts can invite further infection. Always cut at a 45 degree angle to ensure water runs cleanly off the cut. Sanitize your cutting tool in between each cut with rubbing alcohol or a mixture of one part bleach to nine parts water. Burn or dispose the infected material.
Cut out cankers on the trunk bark. Only cut them out, however, if doing so will not threaten the structural integrity of the tree. Trees with cankers that are large enough to girdle the trunk should be removed for safety reasons. Use a clean, sharp knife and cut four inches below and above the canker and two inches on each side. Peel off the infected bark and treat with a fungicide rated for your tree and the specific fungal infection you have. Copper fungicides are generally effective against most fungi, but always read and follow the manufacturer's instructions carefully before applying a fungicide. Once you've cut out the canker, it is important to keep it dry. Cease any overhead watering and cover the wound if wet weather is approaching.
Fungicides are not generally effective against rusts. Proper sanitation and removal of infected material are usually adequate measures for controlling these diseases. You can, however, apply fungicide to wounds as a prophylactic measure against fungal infections. If you wound your tree with the lawn mower, weed eater or any other implement, brush copper fungicide on the wound and keep it dry to help prevent infection.