Size-controlled Si nanopore array with a pore size less than 100 nm is fabricated on Si (100) substrates by using monolayer self-assembled and KOH anisotropic wet etching technique. Morphology and structure of the pores are characterized by SEM and AFM. Results show that a large area of defect-free polystyrene (PS) monolayer film can be obtained when the volume ratio of PS solution to methanol solution is 9:11. A larger volume ratio or a smaller volume ratio will induce similar bilayer structure and defects (point and line) in the PS film, respectively. The lateral size and depth of the nanopore will increase with the etching time, and its morphology will change from circular to inverted pyramid type gradually. But the orderly arranged structure will be destroyed as the etching time is over 10 min. On the other hand, ordered Ge/Si nanoislands and nanorings will be grown on nanopore-patterned Si (100) substrates (inverted pyramid and circular nanopores, respectively) by ion beam sputtering. In addition, reasonable interpretations have been proposed for the formation mechanism of the ordered Ge/Si nanostructure.