Microfluidic devices are state of the art technology which are used for many applications especially as lab-on-chips. Manufacturing and characterization of these devices are reported in literature but process control aspects of vertically aligned multiwalled carbon nanotubes are rarely investigated. Furthermore, nano exchange capabilities with such structures are scarcely studied. In this paper, an industrial quality chemical vapor deposition system is designed, built and controlled. A nonlinear PI controller is employed to control the temperature of the chemical synthesis system, where precise temperature control is crucial. This controller behavior depends on the ratio between the error signal and the reference which enables the controller to act faster while avoiding overshoot. A microfluidic nanoexchanger device is manufactured, flow characteristics are modeled and its nanoexchange capability is tested and proven experimentally. These devices have many applications both in industry and biomedical field. One of the promising applications is building artificial organs such as lungs and kidneys where nanoexchangiss occur naturally. Copyright (C) 2020 The Authors.