We present an updated version of our Monte-Carlo based code for the simulation of ion beam sputtering. This code simulates the interaction of energetic ions with a target, and tracks the cumulative damage, enabling it to simulate the dynamic evolution of nanostructures as material is removed. The updated code described in this paper is significantly faster, permitting the inclusion of new features, namely routines to handle interstitial atoms, and to reduce the surface energy as the structure would otherwise develop energetically unfavorable surface porosity. We validate our code against the popular Monte-Carlo code SRIM-TRIM, and study the development of nanostructures from Ne+ ion beam milling in a copper target.