A method of follow-up decontamination operation for the polluted storage canister of a high activity nuclear waste storage facility, using needle and steel brushes driven by pneumatic tools for abrading the bottom and the inner wall of the storage canister to remove contaminants, a multi-level filter system for air filtration and removing pollutants in the storage canister, and a cover to be used in association with the pneumatic tools and the multi-level filtration system suitable to cap the storage canister, thus effectively block the exposure of contaminant of the storage canister to the external environment, achieving effective decontamination of the radioactive waste and reducing spreading to the environment.