Molecular dynamics simulations of nanoimprint lithography in which a stamp with patterns is pressed onto amorphous poly-(methylmethacrylate) (PMMA) surface are performed to study the deformation of polymer. Force fields including bond, angle, torsion, inversion, van der Waals and electrostatic potential are used to describe the intermolecular and intramolecular force of PMMA molecules and stamp. Periodic boundary condition is used in horizontal direction and Nose-Hoover thermostat is used to control the system temperature. As the simulation results, the adhesion forces between stamp and polymer are calculated and the mechanism of deformation are investigated. The effects of the adhesion and friction forces on the polymer deformation are also studied to analyze the pattern transfer in nanoimprint lithography. The mechanism of polymer deformation is investigated by means of inspecting the indentation process, molecular configurational properties, and molecular configurational energies.