The use of porous templates for controlled formation of nanostructures and nanosystems requires reliable method of pore size, shape, quantity per unit area (porosity), distance to nearest neighbors and porous matrix thickness monitoring. The scanning electron microscopy method allows to estimate these parameters, however, manual processing of obtained images is a very time-consuming task. The use of ImageJ software makes it possible to significantly simplify the process of obtaining detailed statistical information about templates surface. Taking that into account, the work describes in detail the methodology for analyzing of scanning electron microscopy images of SiO2/Si ion-track templates surface to control pore size, shape, unit area and distance to the nearest neighbors. The method for estimating thickness of SiO2/Si ion-track template based on processing of data about surface is also proposed. It is important to note, that the techniques described in this paper not only allow to effectively control SiO2/Si ion-track template pore parameters, but also suitable for other types of porous templates.