High capacity Li-ion batteries are composed of alternating stacked cathode and anode layers with thin separator membranes in between for preventing internal shorting. Such batteries can suffer from insufficient cell reliability, safety and electrochemical performance due to poor liquid electrolyte wetting properties. Within the electrolyte filling process, homogeneous wetting of cathode, separator and anode layers is strongly requested due to the fact that insufficient electrolyte wetting of battery components can cause limited capacity under challenging operation or even battery failure. The capacity of the battery is known to be limited by the quantity of wetting of the electrode and separator layers. Therefore, laser structuring processes have recently been developed for forming capillary micro-structures into cathode and anode layers leading to improved wetting properties. Additionally, many efforts have been undertaken to enhance the wettability and safety issues of separator layers, e.g. by applying thin coatings to polymeric base materials. In this paper, we present a rather new approach for ultrafast femtosecond laser patterning of surface coated separator layers. Laser patterning allows the formation of micro-vias and micro-channel structures into thin separator membranes. Liquid electrolyte wetting properties were investigated before and after laser treatment. The electrochemical cyclability of batteries with unstructured and laser-structured separators was tested in order to determine an optimal combination with respect to separator material, functional coating and laser-induced surface topography.