The beam profile of an electron beam (EB) can be focused onto less than a nanometer spot and scanned over a wide field with extremely high speed sweeping. Thus, EB is employed for nano scale lithography in applied physics research studies and in fabrication of semiconductors. We applied a scanning EB as a control system for a living cell membrane which is representative of large scale complex systems containing nanometer size components. First, we designed the opposed co-axial dual optics containing inverted electron beam lithography (I-EBL) system and a fluorescent optical microscope. This system could provide in situ nano processing for a culturing living cell on a 100-nm-thick SiN nanomembrane, which was placed between the I-EBL and the fluorescent optical microscope. Then we demonstrated the EB-induced chemical direct nano processing for a culturing cell with hundreds of nanometer resolution and visualized real-time images of the scanning spot of the EB-induced luminescent emission and chemical processing using a high sensitive camera mounted on the optical microscope. We concluded that our closed-loop in situ nano processing would be able to provide a nanometer resolution display of virtual molecule environments to study functional changes of bio-molecule systems. (C) 2013 Elsevier Inc. All rights reserved.