Silica nanoboxes synthesized from alumina-rich zeolites, showed two distinct categories of nano-structured materials. Entirely mesoporous nanoboxes (monomodal Al-nanoboxes) were highly thermally and chemically resistant even in the acidic form whereas calcination at high temperature of materials still containing some zeolite remnants (bimodal Al-nanoboxes), resulted in dramatic loss of surface area and pore volume. Pore closure by mobile and amorphous aluminic species was believed to occur. The high thermal and chemical stability of the monomodal Al-nanoboxes was found to be related to the highly siliceous character of the mesopore walls which contained isolated tetrahedral Al atoms linked to tetrahedral Si atoms. Treatment of the acid form of the bimodal nanoboxes with La or Ce containing solutions resulted in quite thermally stable materials owing to the reduction of the number of protonic sites by the rare-earth metal ions.