The treatment in NH4OH of Fe-Silicalite (Fe-MFI) catalysts creates mesopores with a different mechanism with respect to the conventional desilication treatment. A reassembling of Fe-MFI nanocrystals is induced by the creation of isolated defects on the surface of these nanocrystals, as well as a change in the amorphous layer between nanocrystals acting as "glue" to assemble them into larger round-shaped particles occurs. The reassembling process induces also changes in the acidity and hydrophobic character, leading to an enhanced reactivity, and influences the relatives rate constants in the HMF (5-hydroxymethylfurfural) etherification to 5-(ethoxymethyl)furan-2-carbalclehyde (EMF) via acetalization. Moreover, for treatment times with NH4OH longer than 6 h, there is an effective, although minimal, desilication process which leads to a loss of crystallinity, microporous surface area, mesoporosity and acidity characteristics with consequent worsening of the catalytic performances.