The present study demonstrates unidirectional cell migration using a novel 3D microfabricated scaffold, as revealed by the uneven sorting of cells into an area of 1 mm × 1 mm. To induce unidirectional cell migration, it is important to determine the optimal arrangement of 3D edges, and thus, the anisotropic periodic structures of micropatterns are adjusted appropriately. The cells put forth protrusions directionally along the sharp edges of these micropatterns, and migrated in the protruding direction. There are three advantages to this novel system. First, the range of applications is wide, because this system effectively induces unidirectional migration as long as 3D shapes of the scaffolds are maintained. Second, this system can contribute to the field of cell biology as a novel taxis assay. Third, this system is highly applicable to the development of medical devices. In the present report, unique 3D microfabricated scaffolds that provoked unidirectional migration of NIH3T3 cells are described. The 3D scaffolds could provoke cells to accumulate in a single target location, or could provoke a dissipated cell distribution. Because the shapes are very simple, they could be applied to the surfaces of various medical devices. Their utilization as a cell separation technology is also anticipated.