Direct transfer printing of functional materials has been employed in the development of sensors, displays, and energy-harvesting devices. The transfer process can be applied advantageously to depositions onto nonplanar and flexible surfaces at low temperatures. In this work, we fabricated free-standing nanowire arrays and nanomembranes on micrometer-scale trenches by nanotransfer molding. We also investigated how deposition pattern types vary with trench dimensions as well as processing pressure and temperature. Finally, a free-standing polymer membrane fabricated by nanotransfer molding was employed as a novel mask in the preparation of three-dimensional nanodot arrays.