In the field of Nano Technology for the very first time, Microcontroller controlled High voltage power supply and Electrospinning Nanofiber generator is designed. The main purpose of Microcontroller driven Nanofiber generator design is to reduce the unit cost and increase the precision and efficiency. Using this technology, and by varying the collector unit, ultra-thin aligned and non-aligned Nanofibers were engendered. The High voltage power supply takes low voltage as input and generates high voltage and low current as output which are mandatory to stimulate nanofiber. The emphasis of this paper is to elaborate the details of hardware and software design, nanofiber generation technique and the control strategy for stepper motor and plunger movement. This design can be proficiently used in designing high accuracy Nanofiber generators to produce Ultrathin Nanofibers. These Nanofibers are predominantly used in the field of Nano Medicine, Agriculture and Textile Industry.