Linewidth fluctuation of resist patterns is a serious problem in fabricating nanodevices when lithographic resolution is improved to the nanometer scale. As a resist material for reducing linewidth fluctuations, we evaluate hydrogen silsesquioxane (HSQ) with a three-dimensional framework from the standpoints of resist patterning and its ability to reduce linewidth fluctuation. Infrared analyses indicate that SiH bonds in HSQ are broken by electron-beam irradiation, and consequently, the crosslinking required for negative tone patterning is generated. By applying a TMAH developer suitable for the dissolution of the siloxane bonds in HSQ, we improve contrast and reduce the thickness loss of the lightly exposed resist area. In addition, the HSQ resist has relatively high sensitivity for resist materials without any reactive groups. The etching durability sacrificed for the attainment of high sensitivity is improved by oxygen plasma treatment. No damage, such as pattern-shape deformation after the oxygen plasma treatment, is observed. Linewidth fluctuation due to edge roughness of resist patterns results from aggregates in the resist polymer. Aggregates in HSQ are small owing to its three-dimensional framework. In addition, the excellent development property of HSQ avoids any influence from polymer aggregates on development. Consequently, linewidth fluctuation can be reduced to less than 2 nm. This leads to a decrease in the variation of gate capacitance in single-electron transistors.