In this paper we present the Kinetic Monte Carlo simulation system for the simulation of three-dimensional shape evolution with void formation as a model for electrodeposition. The basic system is the Solid-by-Solid model which is an extension of the conventional Solid-on-Solid model for crystal growth to include void formation. The advantage of the Solid-by-Solid model is that complex three-dimensional shape evolution accompanying void formation (from point defects to macro voids) can be simulated without the difficulty of treating moving boundaries. This model has been extended to include the solution part in which the migration of ions is simulated by the coarse-grained random walk. A multi-scale method is employed to generate the concentration gradient in the diffusion layer. The extended model is applied to the simulation of via and trench fillings by copper electrodeposition. Three kinds of additives are included: suppressors, accelerators and chloride ions. The mechanism of void formation, effects of additives and their influence on the bottom-up filling are discussed within the framework of this model. (c) 2013 Elsevier Ltd. All rights reserved.