We propose a process for fabricating nanodot arrays with a pitch size of less than 25 nm. The process consists of localized ion implantation in a metal thin film on a Si wafer using a focused ion beam (FIB), followed by chemical etching. This process utilizes the etching resistivity changes of the ion beam irradiated region that result from metal silicide formation by ion implantation. To control the nanodot diameter, a threshold ion dose model is proposed using the Gaussian distribution of the ion beam intensities. The process is verified by fabricating nanodots with various diameters. The mechanism of etching resistivity is investigated via x-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES).