A system and methods are provided for the therapeutic treatment of brain-plaques, fibrils, abnormal-protein related or aggregation-prone protein related deposition-diseases. The system employs acoustic exposure therapy means for delivering therapeutic energy to at least one brain region. The therapy supports at least one of the following processes: (i) physical breakup, erosion, disentanglement, de-aggregation, dissolution, de-agglomeration, de-amalgamation or permeation of the deposits, (ii) interference in at least one deposit formation process, deposition related chemical reaction or biological or genetic pathway contributing to the deposits or deposition-related processes, and (iii) aiding the recovery, growth, regrowth or improved functionality of brain-related cells or functional pathways negatively impacted by, stressed by or disposed to the deposits, deposition-processes or deposition disease state, or supporting the growth of newly transplanted cells anywhere in the brain-related anatomy. The system and methods treat Alzheimer's and other deposition-related disorders of the brain, with minimal adverse side effects to the patient and may be used in cooperation with a drug.