A novel selective nanoscale etching process that generated a well defined hollow nanostructure was developed by treating manganese oxide nanoparticles with a hydroxylamine solution. This selective etching process was used for exploiting a novel method of differentially functionalizing the internal surface of a hollow silica shell with a catalytically active Mn3O4 layer and creating a novel nanoreactor framework. The nanoreactor fabricated by the newly developed method catalyzed the cyanosilylation reactions of various aromatic aldehydes with size and shape selectivity. Moreover, the substrate selectivity in the cyanosilylation reactions was efficiently tuned by modifying the outer silica shell with silane coupling reagents.