Molecular distillation is an important separation unit. It operates under low pressure and low temperature, assuring no thermal degradation to the molecules. This is an essential alternative, especially for larger molecules. However, the commercial simulator Aspen Plus® does not contain the tool to simulate this process. In this context, this paper aims to compare different tools in the commercial simulator Aspen Plus® to emulate molecular distillation for falling film and centrifugal equipment. A Flash vessel and a rate-based column were used to represent the falling film and centrifugal molecular distillations, respectively. A Flash vessel was used to represent the centrifugal distillation due to its faster residence time. The rate-based column operates at non-equilibrium being suitable to emulate the falling film. The simulation results were compared to experimental data in the literature published by some of the authors of this paper. This study supports the idea of simulating the molecular distillation integrated with other units in the commercial simulator Aspen Plus®. This paper contributes, then, to a way to carry out simulations of this non-conventional process and to a cost-effective process design since the simulation is not fragmented allowing technical economic analyses.