The 3D structural shape-control using Synchrotron Radiation (SR) lithography for the configurations of less than a micron-size has been realized. The fabrication process will be described in details. Moreover, the structure with aspect ratio as high as 4 was achieved. The briefly introduced fabrication process is to deposit a PMMA (polymethylmethacrylate) layer to a silicon substrate by spin coating. The layer is used as the X-ray resist. Subsequently, to expose SR onto the resist through an X-ray mask, then to develop the exposed resist. The principal shape-control is accomplished by optimizing each parameter influencing the resist formation, the exposed SR dosage, and development time. All mentioned above are the parameters determined from the fabrication of an arbitrary shape which is the main purpose in this paper. The targeted evaluation of the fabricated structures is to provide the line and space of 1μm pitch, 1.9μm line-height, and aspect ratio of 4. The technique for optimization of the experimental condition and each parameter for the fabrication process will be explained in the paper. This research is expected to be useful for other related work on manufactures of sub-micron structure. The suggested applications are; a variety of optical elements such as the polarized light beam splitters, diffraction optical elements, and a number of applications in device or system which requires nanoscale structures will find this work employable. The fabrication technique of higher aspect ratio and narrower line-width will be investigated in the future research.