Fine scale microdot arrays of mesoporous silica were achieved by combining ink-jet printing process to Evaporation-Induced Self-Assembly (EISA) of TEOS with Pluronic F127 triblock copolymer as surfactant. It was shown that the addition of 5 mol% of a hydrophobic organosilane, namely TFTS (CF2)CH2CH2Si(OC2H5)3, notably improved the large scale organisation of the mesoporosity by promoting the co-assembly of the surfactant and silica species through the interactions of F127 and TFTS hydrophobic chains. It then let an extra-time for the formation of organized 2D hexagonal domains, and for their realignment before the rigidification of the silica network. Moreover, the control of the initial condensation rate of the sol before deposition allows to get the best organisation of the deposits for a 48h ageing time, which corresponds to the most suitable one both in regards to the co-assembly and silica network rigidification steps. Furthermore, the organization of the microdots was improved by limiting the storage of solvent inside the microdot during the stacking of the layers: this storage can inhibit the structural organization controlled by evaporation and also even degrade the initial organization of the previous layers. By increasing the drying time between two successive layers and reducing the droplet volume, the organization of microdots can be notably improved. By this way, microdot arrays of 25 layers exhibiting a well-organized centred rectangular structure with cylindrical micelles parallel to the interfaces over 80% of their volume were achieved. A promising perspective of our process would be to use a multi-printing-head system to generate multifunctional mesoporous microdot arrays with different grafted functions from one dot to another. Such functionalized arrays could then be used as miniaturized sensors. For instance, silica microdot arrays could host mercaptopropyl groups for heavy metal trapping or semicarbazide groups for peptide grafting or malonamide precursor for actinide trapping. Investigations consisting in the one pot grafting of these different functions by incorporation of the corresponding precursors in a pre-aged sol just before deposition of microdots arrays by ink-jet printing are in progress.