Recently it has been discovered that structural transformations take place on the surface during electrochemical dopig of fullerene layers with alkali metals ions. Nano-scale structures with average size between 20 and 50 nm can be produced at the electrode-electrolyte interface by electrochemical injection of K⁺ and Rb⁺ into the layer. Kinetic Monte-Carlo (KMC) method is used to simulate the formation of nanostructures in K- and Rb-doped fullerene layers. It has been found that phase transformations in the fullerene layer are responsible for the phenomena observed. Thermodynamical phase stability depends on balance between Madelung energy and energy of C₆₀-C₆₀ electronic shells interaction. The method is implemented as portable C and FORTRAN code for UNIX and Windows platforms. Multi-tier design of the application allows to take advantage of location transparency, data integrity and enhanced code re-use. Component object model (COM) support facilates integration with scripting languages and sofware used for data presentation. The dependence of particle size and kinetics of the process on alkali metal content is investigated. Possible applications of the alkali-metal doped fullerene layers as random arrays of nanoelectrodes are considered.