I have worked on dozens of lenses with fungus in them. The best way to prevent fungus is to expose the glass to sunlight from time to time. Fungus, like mold, doesn't tolerate direct sunlight or UV light.
To remove the fungus, I use pure cotton swabs slightly moistened with lens cleaning fluid, and a small amount of toothpaste. Rub the lens with the cotton swab in a small circular motion without applying too much pressure. If the fungus has not fully etched the lens coating, this should remove it.
The most difficult part of the process is getting the lens back together without having dust particles trapped inside. Very careful cleaning and a blow brush are necessary, as well as working in as dust free an environment as you can find.