An organic option for safely removing fungus from fruit trees is a solution of 3 percent hydrogen peroxide and 97 percent water, which does not harm the tree. Apply the hydrogen peroxide with a spray bottle.
Horticultural hydrogen peroxide is typically a 35 percent solution and requires diluting. Mix 2 1/2 tablespoons of the solution with 1 gallon of water. Use a pump sprayer to apply this solution, and apply it on a sunny day so that rain does not rinse the mixture from the tree. Spray the solution onto the top and underside of the leaves until it drips off. Reapply the solution once per week.