This work experimentally demonstrates inline 3D imaging using Structure-from-Motion in microscopic domain. Several microscopic 3D inspection systems exist. A popular method for standard microscopes is Depth-from-Focus reconstruction, which makes use of the shallow depth of field of microscope optics. It requires several scans acquired at different distances of the object along the optical axis. This and other 3D reconstruction methods based on a scanning process are not suitable for fast inline inspection if the scanning direction does not match the object’s transport direction. In this paper we propose a modification to standard microscope optics, which allows for Structure-from-Motion in microscopic domain, by including an additional aperture. The choice of aperture opening and location is crucial to reach the desired lateral and depth resolution. This paper investigates the optimal choice for these parameters to match a desired application, in this case the inspection of a metallic surface with 4 mm resolution in all three dimensions. The choice based on theoretical considerations is successfully tested in an experimental setup. Results are compared with a reference measurement from confocal microscopy.