Nanoporous materials are of great importance in a variety of applications such as heterogeneous catalysts because of their large specific surface area and tuneable porosity. Herein, we proposed an approach for rationally designing nanoporous materials on a substrate by lithography, co-sputtering and selective dissolution. The physical processes (i.e., lithography and sputtering) were used to design shapes and arrangements of nanostructures, and the chemical dissolution process was used to form nanopores inside the nano-patterns. In order to investigate the compatibility of the sputtering and selective etching with the lithography process, we formed patterned nanoporous Au by co-sputtering of AuCu followed by selective dissolution of Cu with acid. Interestingly, using this process, dish-shaped Au nanostructure arrays formed through lithography processes were successfully decorated with nanoporous Au, resulting in the enhancement of SERS intensity by 10 times. Then, in order to show the versatility of our approach, we synthesized nanoporous SiO2 patterns. In this case, nanoporous SiO2 was synthesized by co-sputtering of SiO2 with Cu followed by selective dissolution of Cu with acid. Because of removal of the thermal process, this SiO2 synthesis appears to be compatible with a variety of nanofabrication procedures. Finally, in order to investigate further merits of the use of sputtering, we demonstrated the synthesis of dendritic Pt nanoporous particle arrays by co-sputtering and acid treatment. Interestingly, nanoporous particle arrays, i.e., hierarchical structure, were formed from PtCu crystal grains without coagulation, showing a possibility that crystal grains can play a role in the formation of hierarchical nanostructures.