Vertically aligned mesoporous silica films can be generated by electrochemically assisted self-assembly (EASA) but the accurate control of their thickness is essentially restricted to the 100 nm range. Here we have developed a wet etching approach using dilute ammonium fluoride to gradually decrease the thickness of ferrocene-functionalized films down to 20 nm by increasing the etching time. The effectiveness of the process was followed by monitoring the decrease in the voltammetric response of ferrocene moieties that are progressively removed from the electrode surface upon silica etching. Film thickness variations have also been confirmed by profilometry and were consistent with the electrochemical measurements. Electron microscopy analyses indicated a uniform thickness decrease but also some loss in the integrity of the mesostructure after prolonged etching.