The Scanning Electron Microscope (SEM) as 2D imaging equipment has been widely used in biology and material sciences to determine the surface attributes of a microscopic object. Having 3D surfaces from SEM images would provide true anatomic shapes of micro samples which allow for quantitative measurements and informative visualization of the systems being investigated. In this contribution, we present a Differential Evolutionary (DE) approach for both SEM extrinsic calibration and 3D surface reconstruction. We show that the SEM extrinsic calibration and its 3D shape model can be accurately estimated in a global optimization platform. Several experiments from various perspectives are performed on real and synthetic data to validate the speed, reliability and accuracy of the proposed system. The present work is expected to stimulate more interest and draw attentions from the computer vision community to the fast-growing SEM application area.