Ultrathin block copolymer films are promising candidates for bottom-up nanotemplates in hybrid organic-inorganic electronic, optical, and magnetic devices. Key to many future applications is the long range ordering and precise placement of the phase-separated nanoscale domains. In this paper, a combined top-down/bottom-up hierarchical approach is presented on how to fabricate massive arrays of aligned nanoscale domains by means of the self-assembly of asymmetric poly (styrene-block-ethylene/butylenes-block-styrene) (SEBS) tirblock copolymers in confinement. The periodic arrays of the poly domains were orientated via the introduction of AFM micromachining technique as a tool for locally controlling the self-assembly process of triblock copolymers by the topography of the silicon nitride substrate. Using the controlled movement of 2- dimensional precision stage and the micro pressure force between the tip and the surface by computer control system, an artificial topographic pattern on the substrate can be fabricated precisely. Coupled with solvent annealing technique to direct the assembly of block copolymer, this method provides new routes for fabricating ordered nanostructure. This graphoepitaxial methodology can be exploited in hybrid hard/soft condensed matter systems for a variety of applications. Moreover, Pairing top-down and bottom-up techniques is a promising, and perhaps necessary, bridge between the parallel self-assembly of molecules and the structural control of current technology.