High aspect ratio three-dimensional micro- and nanopatterns have important applications in diverse fields. However, fabricating these structures by a nanoimprinting method invites problems like collapse, dislocation, and defects. Finite-element analysis (FEA) is a good approach to help understand the filling process and stress distribution. The FEA method was employed to simulate the nanoimprinting process using positive and negative molds with aspect ratios of 1:1, 3:1, 5:1, and 7:1. During the filling process, the resist adjacent to boundaries has the maximum displacement. The corners of contact areas between the protruding part of the mold and the resist has the maximum Von Mises stress. For both positive and negative molds, the maximum stress in the mold increases with aspect ratio. However, filling up negative molds is more difficult than positive ones. With the same aspect ratio, the maximum stress in a negative mold is approximately twice as large as that in a positive one.