Advanced directed-self-assembly (DSA) has been deployed to form vertical cylindrical structures inside deep Si trenches and via with the cylinders' width at nm-scale for making electrical interconnection in the vertically stacked 3D-LSIs/ICs. DSA reaction for PS(57k)-b-PMMA(25k) diblock copolymer (DBC) with PS:PMMA ratio as 2:1 have resulted into the formation of 20 nm-width nano-cylinders (NC) running parallel and straight up to > 7 μm inside the 10 μm-deep Si trenches. Upon increasing the molecular weight of PS from 57k to 140k (keeping the ratio of DBC as 2:1), the width of NC has enlarged from 20 nm to > 80 nm. A ~100 nm-width metal interconnects were formed inside the ~500 nm-width via of the bonded 3D-ICs, for Sn and In metals. Based on Self Consistent Field theory, both 2D & 3D simulation results showed that the metal particles attached to PMMA of DBC are connected vertically and forms cylinder, as long as the metal particles are well attached to PMMA.