Top-down lithography based on secondary sputtering lithography can provide high resolution (10~30 nm) and high aspect ratio (>20) in nanopattern. This technique can fabricate various shaped nanopattern and use various materials, so that secondary sputtering lithography is useful to self-assembly of soft materials and multimetallic system. Self-assembly of soft materials is essential to various applications such as liquid crystal display, photonic crystals, polarizer, and nano patterning. Multimetallic system in nanoscale is also important for potential applications such as photonic devices, electronics, and catalysis. For those applications, in this work, precisely controlled secondary sputtering lithography was developed. To control alignment of liquid crystal, tilted line pattern and high density nanopattern using block copolymer were developed. As another soft material, dendrimer was also aligned along the nano pattern, which is firstly reported parallel alignment. Self-assembly in nanopattern based on secondary sputtering lithography can be achieved with very small dead space (1~2%) and high uniformity. As second development, multimetallic system using secondary sputtering lithography has no limitation in selection of materials and provides small grain boundaries (< 10 nm). Multimetallic nanostructures were used to catalysis and hydrogen gas sensor, which resulted in enhanced performance such as faster catalytic reaction and fast response time in gas sensing. Improved secondary sputtering lithography can be utilized to potential applications such as self-assembly templates, multimetallic catalysis and gas sensors.