The removal of alkyltrimethylammonium template from MCM-41 ordered silica was investigated, using positron annihilation lifetime spectroscopy (PALS). The lifetime spectra of positrons were measured as a function of temperature for several samples with different template alkyl chain length (different pore radius). At low temperatures the template interior behaves like a liquid, and the "bubble model" of positronium in liquid can be applied. The change of template structure starts at 380-400 K, and at 520 K the process of template removal is completed. Analysis of o-Ps lifetime components suggests the following stages: breaking long micelle cylinders, rise of the gaps between the fragments, and pore evacuation.