Disclosed are thermotherapeutic compositions for treating disease material, and methods of targeted therapy utilizing such compositions. These compositions comprise a) stable single domain magnetic particles; b) magnetic nanoparticles comprising aggregates of superparamagnetic grains; or c) magnetic nanoparticles comprising aggregates of stable single magnetic domain crystals and superparamagnetic grains. These compositions may also comprise a radio isotope, potential radioactive isotope, chemotherapeutic agent. These methods comprise the administration to a patient's body, body part, body fluid, or tissue of bioprobes (energy susceptive materials attached to a target-specific ligand), and the application of energy to the bioprobes so as to destroy, rupture, or inactivate the target in the patient. Energy forms, such as AMF, are utilized to provide the energy. The disclosed methods may be useful in the treatment of a variety of indications, including cancers, diseases of the immune system, central nervous system and vascular system, and pathogen-borne diseases.