Thermo-fluid properties are required for numerical modeling of nano/micro devices. These properties are mostly obtained from the results of molecular dynamics (MD) simulations. Therefore, efforts have been made to develop methods for numerical evaluation of fluid properties such as pressure and velocity. One of the main challenges faced by numerical simulations is to simulate steady molecular flow in channels with non-equal inlet and outlet boundaries. Currently, periodic boundary conditions at the inlet and outlet boundaries are an inevitable condition in many steady flow molecular dynamics simulations. As a result, a nano-channel with different cross sectional areas at the inlet and outlet could not be simulated easily. Here, a method is presented to generate and control steady molecular flow in a nano-channel with different cross sectional areas at the inlet and outlet. The presented method has been applied to a converging-diverging channel, and its performance has been studied through qualitative and quantitative representation of flow properties.