In this work, we simulate and optimise an industrial distillation system to produce bioethanol manipulating design parameters to reduce the total exergy loss inside the columns and taking into account the economic parameters. The operational parameters are validated using Aspen Plus through the analysis of the exergy loss profile. However, the variation of the number of stages is not straightforward in processes simulators because requires to evaluate the optimal position to insert the stage in the column (i. e., stripping or rectification section). It is demonstrated that the number of stages tightly impacts the energy efficiency of the columns. The optimisation is realised in Matlab to relate the total exergy loss inside the columns with its cost identifying the sections with greater exergy loss, inserting new stages (defined by the user) and calculating the capital cost associated. The results show that is possible thermodynamically optimise the industrial distillation system.