Results concerning the structural consequences of template removal from MCM-41 mesoporous materials are described using ozone, N2O and NO2 as oxidants in comparison with the conventional method applying oxygen. Si, TiSi-, VSi and ZrSi-MCM-41 samples were synthesized by the usual methods. For characterization of the as-synthesized and treated samples XRD, nitrogen adsorption and IR-spectroscopic methods were used. The catalytic activity of the samples was tested in the Friedel-Crafts alkylation of toluene by benzyl chloride. The comparison of template removal agents showed that ozone was the most active at low temperature (423 K), and the treatment was less destructive than burning off the template in oxygen. Nitrogen oxide treatment (NO2 and N2O) resulted in template removal at relatively low temperature (573-623 K), and,structure deterioration was small. IR spectra taken in the framework vibration range revealed that more original -SiOH groups remained ashydroxyl nests, furthermore, the heteroatoms remained in tetrahedral coordination after ozone and nitrogen oxide treatment compared to burning off the template by oxygen. The results proved the advantages of ozone or nitrogen oxide treatments: (i) gentler to heteroatoms situated in the framework of the materials, probably leaves them intact, (ii) does not result in the formation of secondary micropores which would decrease the uniform arrangement of the original pore systems, (iii) by preserving the active centers in their original coordination more uniform product distribution may be expected in catalytic reactions.