In this presentation we are going to show the results on polyelectrolyte multilayers systems (PEM, polyeletrolyte membranes) studies. Obtained in the layer-by-layer self-organization process (LbL) membranes can be proposed for several applications. One of the most spectacular is the use of PEM in cell transplantation. Encapsulated cells are protected against the immune attack by recipient organism. The respective polyelectrolyte properties which forms the multilayer system has a large impact on the PEM character, while the used membrane will influence the cell, affecting its shape, or changing the form and strength of interaction with the environment. Atomic Force Microscopy (AFM) can help us to characterize several properties of the produced multilayers. The morphology and thickness determination for multilayers based on poly-L-lysine, polyethylenimine and polystyrene sulfonate will be discussed.