Two-dimensional polyethylene terephthalate nanochannels with dimensions of around 80 nm width and 250 nm depth were imprinted precisely into a polyethylene terephthalate sheet with optimized hot embossing parameters. Deformation of the polyethylene terephthalate nanochannels was investigated by both experiments and simulation. The orthogonal method was employed for both simulations and experiments. The replication accuracy was evaluated by a method based on weighted average. Comparison of the replication accuracy between experimental data and simulation results shows good agreement and confirmed the developed simulation method. It is expected that the developed simulation method has high potential in the hot embossing process analysis for the viscoelastic case.