An ultrahigh vacuum (UHV) operating scanning tunneling microscope (STM) has been designed and built with the aim of studying surfaces irradiated with low energy ions. Because the low energy ion implanter was sited in a location remote from the STM laboratory, it was also necessary to design and build a portable vacuum system which was capable of interfacing with both the ion implanter and the STM chamber, and thus, effect a sample transfer under UHV. This article presents a description of the STM and a selection of recent research results which demonstrate the capabilities of the system. In particular, the article reports on the development of small‐scale structures on graphite, platinum, and copper surfaces after irradiation with low‐energy helium ions and on the growth of copper islands formed by ion beam deposition on graphite substrates.