The separation of microscopic encapsulates is an area of increasing importance due to applications in a wide variety of fields ranging from the production of cosmetics and pharmaceuticals to the search for new molecules and genetically-modified microorganisms. Major challenges are related to the proximity in physicochemical properties of the encapsulating material and the suspension media. This is the case for encapsulation into polymeric capsules and lipid-based systems such as liposomes. We are particularly interested in liposomes as they can be useful in model studies of the interaction between molecules and organisms with lipid bilayers, which represent possible interactions with cells. In this regard, we have recently started a research program for the search of translocating peptides by using a surface display system that locates the possible candidate molecules on the surface of yeasts. To determine whether a candidate exhibits translocating abilities, the yeasts with the displayed peptides need to come in contact with liposomes and as a result, they might end up encapsulated. At this point, the encapsulated need to be separated out and collected for further analyses. An attractive route for separation is microfluidics as they permit control over flow rates and interaction times. Here, we explored in silico an asymmetric pinched Flow fractionation (AsPFF) microfluidic system for the separation of particles in the range of 50 and 500 µm. The simulations involved the particle tracing module in COMSOL multiphysics with the aim of mainly separating yeasts of 50 µm and liposomes of 200 µm with the encapsulated yeasts. We investigated flow rate ratios in the range of 1:25 to 1:50 over the 11 different outlets of the system (see Figure below). The results show separation efficiencies above 90%, which are very encouraging and open the opportunity to further explore this microfluidic system experimentally via low-cost manufacturing in the laser cut PMMA devices that we have developed over the past few years in our group. Moreover, this opens the opportunity for improving separation efficiencies in other biological and biomedical applications of interest.