Morphological changes in thin film patterns of a positive-tone electron beam resist induced by sequential infiltration synthesis and solvent annealing were revealed by atomic force microscopy for the fabrication of silica imprint molds with sub-15 nm trenches. In sequential infiltration synthesis, the wiggling of 40-nm-thick resist film patterns was attributed to decreasing the widths of the resist terraces and baking at 100 °C rather than exposure to a vapor of trimethylaluminum. Reducing the thickness of the resist film from 40 nm to 20 nm prevented the wiggling of resist film patterns after sequential infiltration synthesis. Solvent annealing with a toluene vapor at 20 °C increased mouse-bite defects appearing at the line edges of the resist film patterns, and significantly increased mouse-bite and line-break defects of silica imprint molds after dry etching. These results suggest that the polymer/substrate interface had a significant impact on the morphological fidelity of resist film patterns during electron beam lithography procedures.