Abstract: A system and method for controlling contamination of harmful substances such as fungi in structures, which comprises the aspects of controlled evacuation of contamination in cavities within a structure, removal of the source of contamination at hard-to-reach structures in a substantially non-destructive manner, and treatment of contaminated surfaces to prevent re-contaminations. Controlled evacuation may be facilitated by creating a pressure gradient in a contaminated cavity, such as by drawing air through one or more inlets and outlets created in the structure while maintaining relatively safe containment of the contaminated air. The drawn air may be filtered to remove contaminants. The substantially non-destructive source removal process may include the use of biocide or microwaves to abate the mold colony in hard-to-reach structures. The surface treatment process comprises the application of a lock-down material to prevent re-contaminations.