A method of treating cancerous or benign organ disorders by selectively irradiating organ tissue with focused energy is disclosed. The method comprises the steps of: inserting an E-field probe sensor at an appropriate depth in the organ tissue, monitoring the temperature of the skin surface near the organ (if focused energy is used), placing two or more energy applicators around the organ, Set the initial power level delivered to each energy applicator, set the initial relative phase delivered to each energy applicator to focus energy on the E-field detector located in the organ tissue (if focused energy is used) , delivering energy to two or more energy applicators to selectively irradiate organ tissue and treat at least one cancerous and benign organ condition with focused energy, adjusting delivery to each energy applicator based on monitored skin temperature during treatment monitor the energy delivered to the energy applicator, measure the total energy delivered to the energy applicator during treatment and display the total energy in real time, and deliver the desired total energy dose through the energy applicator Treatment is complete upon delivery to the organ. Focused or unfocused energy can be used as a preferred energy source with a microwave energy applicator. However, any combination of energy applicators such as electromagnetic, ultrasonic, radiofrequency, and laser may be used together to form focused energy. Unfocused energy can be combined with focused energy to enhance thermotherapy. Several applications for breast cancer treatment include treatment of advanced and early breast cancer, prevention of breast cancer, and treatment of benign breast disease and ductal carcinoma in situ.