Despite many available models at different reactor length scales, no models exist for designing homogeneous-heterogeneous reactors from first principles by linking molecular with macroscopic scales. Hybrid algorithms, based on a domain decomposition method, are proposed to couple a continuum fluid-phase transport/reaction model with a new efficient, real-time surface Monte Carlo model suitable for stiff problems. These algorithms properly treat surface heterogeneities and morphology and provide the exact boundary condition to the continuum fluid-phase model. In this way, molecular-scale information is integrated into a macroscopic chemical system. The methods are applied at atmospheric pressure to a stagnant boundary layer near a catalytic surface where heterogeneities are caused by adsorbate-adsorbate interactions. Both steady-state and transient simulations are performed Such numerical methods have the potential for microscopic control of chemical processes through macroscopic control of experimental parameters. Applications to homogeneous-heterogeneous processes such as catalytic reactors, control of morphology of solid materials with atomic resolution, and corrosion processes are also discussed.