We discuss experimental issues associated with a novel operating mode of scanning ion conductance microscopy (SICM). This mode characterizes the ion fluxes that emanate from conducting polymers (CPs) as they actuate, important for understanding CP applications ranging from artificial muscles to micropumps. The CP studied is a thin film of poly (3,4-ethylenedioxythiophene) (PEDOT) actuated out of plane. We outline the design principles underpinning our CP ion flux measurements and discuss experimental complications that arose - most notably a baseline current that may be attributable to a spatially varying CP oxidation state. We discuss the dependence of this baseline ion flux current on the separation distance between SICM tip and CP film, substrate type and substrate area.