Silicon dioxide (SiO2) has been the most important insulator in the highly-developed field of silicon (Si) technology. Accurate pitch and gate linewidth measurements for SiO2/Si systems (systems with a SiO2 insulating layer and Si substrate) have become necessary. Studying one such system obviously presents different results from that of the widely researched Si/Si structure, because the edge profile of the secondary electron (SE) signal contains contributions from two materials. In this work, several scanning electron microscope (SEM) images and SE profiles of SiO2/Si pitch and trapezoidal line structures, using various geometric and experimental parameters, were simulated through the use of Monte Carlo (MC) methods. It was found that, in contrast to Si/Si systems, the height of the insulating layer cannot be ignored during the evaluation of pitch and linewidth. The thickness (i.e., height) factor does play an important role in the contrast of SEM imaging and the shape of the SE profile in these two-material systems. The mechanism of the influence of insulating layer thickness for imaging was studied in detail. In addition, the SiO2/Si pitch structure with a real rough surface was also studied. This work has significant implications for the study of various kinds of two-material systems and could help to optimize the pitch and gate linewidth measurements.