Recently, the application of inorganic nano-periodic structures has become an active area of research. Polysilsesquioxane (PSQ) is known as a hydrolytically stable organic-inorganic hybrid material and this study proposes RT nanoimprint using methylated poly silsesquioxane (Me-PSQ) dissolved in a high-boiling solvent. PSQ electron beam cross-linked by a high electron beam irradiation maintained the shape of nanopatterns and enhanced the heat resistance. As a result of the analysis of the Fourier transform infrared spectrophotometer (FT-IR), a siloxane linkage (Si-O-Si bridging) constitutes a core element of PSQ. The peak wavenumber of Si-O-Si bridging at cross-linked PSQ by electron beam irradiation shifted from 1115 to 1135 cm−1. The peaks shifted towards the high wavenumber side and approached the second peak (1170 cm−1) of the Si-O-Si stretching vibration of quartz. This result suggests that the physical properties of electron-beam irradiated PSQ approach those of quartz.