A distortion correction technique is presented to enhance the 3D scanning performance of a micro-size camera-projector system. Recently, several types of micro-size digital projectors and cameras are available. However, there have been few effort to develop a micro-size 3D scanning system. We develop a micro-sized 3D scanning system which is based on the structured light technique. Three images of phase-shifted sinusoidal patterns are projected, captured, and analyzed by the system to reconstruct 3D shapes of very small objects. To overcome inherent optical imperfection of the micro 3D sensor, we correct the vignetting and blooming effects which cause distortions in the phase image. Error analysis and 3D scanning results on small real objects are presented to show the performance of the developed 3D scanning system.