Fire Blight is a very difficult infection to control once it has gotten into an orchard. If you have caught it early enough you may be able to stem the spread, but complete irradication is doubtful. Carefully disinfecting your pruning tools between EVERY cut, EVERY time, remove all infected branches, cutting them off at least 6" below the visible infection. If you see darkened patches in the interior wood, remove another 3" until you are cutting into clean wood. Be scrupulous about disinfecting the pruners between EVERY cut (here is an excellent description of good pruning hygiene: http://baker.ifas.ufl.edu/Horticulture/documents/DisinfectingPruningTools.pdf
Dispose of all pruned infected branches by burning, burying, or placing in curbside garbage pick-up. Do not leave them on the ground or in your compost pile.If there are wild cherries or apples or other members of the apple family near your orchard, it is best to remove them completely.
This regime will help slow the infection, but it is nearly impossible to stop it. You may eventually have to replace the orchard, at which time it would be worth planting blight-resistant varieties. For more detailed information here is an excellent fact sheet on fire blight and its control: http://extension.colostate.edu/topic-areas/yard-garden/fire-blight-2-907/