As the importance of three-dimensiona (3D) nano patterns and structures has recently emerged, interest in the study of 3D structures of block copolymers has increased. However, most existing studies on block copolymer 3D patterns on substrates are limited to simple 3D structures such as a multi-layered forms. In this study, we propose an experimental method for realizing free-standing 3D block copolymer patterns on substrates using an e-beam lithographic template and film transfer method. The block copolymer 3D structure formed in wide hole templates are similar to simple multi-layered structures; however, as the width of the hole template become narrower, more complex block copolymer 3D structures are formed in which the upper and lower layer structures are interconnected. Furthermore, we introduce a method to fabricate novel block copolymer structures in which the 2D planar structures are connected to 3D complex structures. Proposed 3D block copolymer fabrication method provides a framework for generation of unconventional 3D structures of block copolymer, which can be useful for next generation 3D devices.