In this study, we investigated the possibility of forming the fine Si dot arrays by means of electron beam (EB) lithography and dry etching technique for the future’s devices with nano-scale structures. We examined the properties of Ar ion milling for the fabrication of nanometer sized Si dot arrays on a Si substrate. We have succeeded in forming 40 nm pitched Si dot arrays with a diameter of <20 nm using dot array patterns of the calixarene resist as a mask. We also obtained the Ar ion milling property that there exists the horizontal milling rate as well as the vertical milling rate. We formed Si dot arrays with a dot diameter of about 10 nm using this property. It was clarified that Ar ion milling and EB lithography with calixarene resist has the potential to form Si nano dot arrays for the nano devices.