Using experimental techniques along with computational fluid dynamics and electrodynamic simulations the performance of the first of three focusing elements in an electrospray macromolecular patterning system was assessed. The performance of this element, the ion funnel, was analyzed by varying the parameters and electric field applied to the system including electrospray emitter to atmosphere-vacuum interface capillary distance, temperature of the desolvating heater, injection rate of solution and the voltage applied to the jet disruption element. Results indicated that processes involved in injecting larger droplets into the chamber resulted in a less effective transmission of the ions through the funnel. Droplet diameter was increased by increasing flow rate and was decreased by increasing the desolvation heater. Varying the voltage applied to the jet disrupting element indicated a peak transmission voltage, when using a 20 mil interface capillary,of 175 V and when using the 30 mil capillary of 180 V. Numerical simulations were in agreement with these values although the widths of these transmission curves were much narrower than the experimental curves.