In this paper, nano manufacturing using the FPN (Fountain Pen Nano-Lithography) with active membrane pumping is investigated. This FPN has integrated pumping chamber, micro channel, and high capacity reservoir for continuous ink feed. The most important aspect in this probe provided the control of fluid injection using active membrane pumping in chamber. The flow rates in channel by capillary force are theoretically analyzed with two different working fluids, DPD (diphenyldichlorosilane) and water, including the cantilever deflection and the control of mass flow rates by the deflection of membrane. The theoretical results are compared with numerical ones that calculated by commercial code, FLUENT.