In a previous post I mentioned some of the diseases that attack apples. Rots can be cut out, but most of the time the summer rots will make the fruit useless. Sooty blotch and fly speck grow on the surface of the fruit and, therefore, can be removed without affecting the fruit much.
One of the methods that commercial growers might use is to soak infected apples in a chlorine solution. After soaking the apples, the fruit is them brushed to remove any residue. These pictures show a before and after image of apples that were treated with a chlorine solution. The amount of chlorine used will depend on the formulation and concentration of the product. You should be aware if you use a product such as Chlorox, that you may be in violation of pesticide laws. Also you may leave unwanted residue on the fruit.
The safest way to remove sooty blotch and fly speck is to simple peal the fruit. In some circumstances, the diseases can be rubbed off with water and a cloth. In either situation, the flesh of the fruit should be fine.