The molecular stencil patterning (MSP) technique is a new surface molecular engineering technique developed for cation-templated porous silicas to graft several functions with vicinity control. First, tetramethylammonium ions (TMA(+)) are introduced by ion exchange of the cetyltrimethyl-ammonium template (CTA(+)). Then, the coverage is controlled to create a masking array of cations, the pattern of which is produced by mutual electrostatic repulsion. A first function is grafted, here monopodal trimethylsilyl groups (TMS) or dipodal ethyl-1,2-bis(dimethylsilyl) (EBDMS) groups. After the removal of the masking cations, a second function is grafted using here N-(2-aminoethyl)-3-amino-propyltrimethoxysilane precursor. The distribution of N-(2-aminoethyl)-3-amino-propylsilyl functions (AAPS) is probed by complexation to Cu(ii) ions. X-Ray diffraction, N(2) adsorption-desorption isotherms, (13)C solid-state NMR, IR, UV-visible and electron paramagnetic resonance (EPR) techniques show that MSP can produce isolation of AAPS by TMS, or even better by EBDMS groups, with preservation of the silica pore structure.