Abstract Multilevel and three-dimensional (3D) patterning eliminates more complicated steps in the fabrication processes of micro and nanoscale structures. Multiple lithography processes with inter-level alignment or single lithography with multi layer resist is essential for three-dimensional patterning. Nanoimprint lithography has demonstrated the potential of 3D patterning in a single step. A number of 3D structures have found immediate applications in a range of microelectronic systems such as microoptics, microelectromechanical systems, and monolithic microwave integrated circuits [Appl. Phys. Lett. 78 (2000) 3322; Appl. Phys. Lett. 79 (2001) 2285]. In this work, electron beam lithography (EBL) with different doses followed by reactive ion etching (RIE) is employed in the fabrication of multilevel structures of SixNy molds. The multi level patterns have been transferred into the mold in single step RIE. The imprint process has been performed below the glass transition temperature of the polymer. This may alleviate the alignment errors due to different thermal expansion coefficients in various materials.