In this paper, a comprehensive consideration for the optimization of the Active Fountain Pen Nanolithography (AFPN) device is presented. The material and the dimensions of the device are chosen for the final fabrication. First, the effect of the capillary pressure is analyzed. In this device, the ink is directed into a channel by capillary pressure which is inversely proportional to the size of the channel. When the size of channel is very small, the capping layer of the channel will deflect and cavitations will probably occur in the chamber due to the capillary pressure. However, with the correct structural design and an adequate channel material, the cavitations and the deflection of the channel can be greatly reduced. With this in mind, we increased the size of the device for ease of the fabrication and to avoid cavitations. The pumping performance is simulated under the actual deflection of the membrane by FLUENT. The results show that the mass flow rate at the outlet is dependent on the amount of membrane deformation. As a final step, the state of the ink at the tip after it fills the device is simulated, with SiN showing the best performance in decreasing the amount of ink on the tip.