The results of an experimental and computational investigation of the selective separation of carbohydrates on nano-membranes in cross-flow filtration are reported. Two commercial membranes (NF270-400 and TFC-SR3) were characterised in terms of permeability and rejection of carbohydrate solutions. It is shown that the membranes can be used to recover glucose and galactose from their mixtures with lactose. The permeate flux is shown to depend on sugar concentration, with permeate flux decreasing as the concentration increases. Quantitative evaluation using numerical analysis of the above flow and separation process showed that the performance of nano-membranes can be captured and reproduced with sufficient accuracy, thereby reducing the number of experiments require to evaluate the suitability of membranes in different applications. A Fickian approach is adopted to model the separation, and is shown to be effective.