A new automated molecular modeling method was developed to locate coke molecules and to follow their growth inside zeolites using the Cerius2 software from MSI. This method is based on the consecutive use of isothermal molecular dynamic (NVT), Monte Carlo simulation (sorption), and energy minimization procedures. The Cerius2 software scripting capacity combined with the Tool command language (Tcl) is used to automate the procedure. The results obtained on the location of coke molecules formed during toluene transformation at low and high temperatures demonstrate the interest of the method. Moreover, the sorption procedure used here is particularly useful to specify the mode of growth of cake molecules formed inside the zeolite pores.