We learned earlier what causes wood rot, now lets repair it.

Dealing With Decay
The first and most important thing to do once decay is discovered is to figure out where the water is coming from. Check for the obvious - roof and plumbing leaks, and missing or punctured flashing. Look for stains and drip tracks caused by ice dams. Are eaves wide enough to prevent water from cascading down sidewall's? Are gutters poorly maintained or missing? Do finish grades slope towards or away from the foundation? Are foundation cracks admitting water? Is untreated wood in direct contact with concrete, masonry, or soil? Check to see if crawl spaces have soil covers, and if venting and/or insulation is present, adequate, and properly placed. The same goes for attics. Peeling and blistering paint often signal inadequate interior ventilation, or a missing vapor retarder. Water stains on framing and sheathing inside walls suggest condensation. Remember that to make the remedy permanent, you've got to cure the disease -water infiltration, not just treat the symptoms- mildew, mold, and decay.

Once the source of water has been eliminated, remove as much decayed wood as is practical and economical.
This is especially important with girders, columns, and other critical members whose load-carrying ability may have been compromised. There's no known way of accurately determining the remaining strength of decayed wood left in place. Cut back rotted members to sound wood, keeping in mind that difficult-to-detect incipient decay can extend well beyond visibly rotted areas. When a partially decayed structural member can't be replaced, reinforce it with a "sister" anchored to sound wood. Decayed wood absorbs and holds water more readily than sound wood, so let rotted areas of members not removed dry out before making repairs and closing in. Otherwise, you're just adding fuel to the slow fire.
In damp crawl spaces or other places where water is likely to appear, replace decayed members with preservative treated wood. The major model building code agencies -BOCAI, ICBO, and SBCCI- require that treated wood be used for sills and sleepers on concrete or masonry in ground contact, for joists within 18 in. of the ground, for girders within 12 in. of the ground, and for columns embedded in the ground supporting permanent structures.
In-place treatment with borates
Dormant fungi can be reactivated when dry, infected wood is re wetted. Consider treating infected, but otherwise serviceable wood left in place with a water-borne borax-based preservative that will not only kill active fungi, but guard against future infection as well.
An effective homemade version of Bora-Care is   "HERE"

Borates have low toxicity to humans and are even approved for interior use in food processing plants. They don't affect wood's strength, color, or finish ability, don't corrode fasteners, and don't outgas vapors. Widely used in treating new timbers for log homes, they're the preservative of choice for remedial treatment of wood in service. Because of the decay hazard posed whenever wood bears on concrete or masonry, solid borate rods are often inserted into holes bored near contact areas. Should wood ever get wet, the rods dissolve and ward off infection. Infected wood can be treated with
Boric Acid an extremely effective cure for a multitude of problems including control of wood rot in homes and boats and it is natures insecticide for control of fleas,roaches,termites,ants,spiders and many other household pests.
Before any repairs or replacement of damaged wood is started,
I recommend a through treatment of damaged areas with Boric Acid to eliminate future problems and stop the spreading of the fungi.

Epoxy repair of decayed wood
Sometimes replacing rotted wood isn't an option. In conserving historic buildings, for example, the goal is to preserve as much of the original "architectural fabric" as possible. Stabilizing deteriorated wood with epoxy is often the only choice. Epoxies consist of resin and hardener that are mixed just before use. Liquids for injection and spatula-applied pastes are available. After curing, epoxy-stabilized wood can be shaped with regular woodworking tools and painted. Epoxies are useful for consolidating rotted wood, restoring lost portions of molding's and carvings, and for strengthening weakened structural members. In the last case, they're used to bond concealed metal reinforcement inside holes or channels cut into hidden faces. Epoxies aren't preservatives and won't stop existing decay or prevent future infection. They can be tricky to use; follow the manufacturer's mixing, application, and safety instructions to the letter.