Based on the local energy dissipation property of the molecular beam epitaxy (MBE) model with slope selection, we develop three, second order fully discrete, local energy dissipation rate preserving (LEDP) algorithms for the model using finite difference methods. For periodic boundary conditions, we show that these algorithms are global energy dissipation rate preserving (GEDP). For adiabatic, physical boundary conditions, we construct two GEDP algorithms from the three LEDP ones with consistently discretized physical boundary conditions. In addition, we show that all the algorithms preserve the total mass at the discrete level as well. Mesh refinement tests are conducted to confirm the convergence rates of the algorithms and two benchmark examples are presented to show the accuracy and performance of the methods.