Numerical simulation codes are basic tools for designing Free Electron Lasers (FELs). This paper describes a numerical method for the time-dependent, three-dimensional simulation of the free electron laser (FEL) using a rectangular waveguide within overmoded configuration when the radiation wavelength is much shorter than the waveguide cut-off wavelength. Instead of developing a new code, the GENESIS simulation code is modified for our purpose. This method presented here can be used for extending the capacity of GENESIS to cover this special configuration. The major modification is to apply the metal boundary conditions on the field equations in a limited rectangular region and the full Cartesian mesh using the Alternating Direction Implicit (ADI) integration scheme to solve the field equation remains adopted.