The problem of online system identification and control of microscopic processes is considered. Traditionally, such processes are numerically simulated employing atomistic simulations. The unavailability of closed-form models to describe the evolution makes the controller design task challenging. A methodology is developed in which subspace algorithms for bilinear system identification are coupled with feedback linearization techniques with objective the online identification and control of microscopic processes. We illustrate the applicability of the proposed methodology on a Kinetic Monte Carlo (KMC) realization of a simplified surface reaction scheme that describes the dynamics of CO oxidation by O2 on a Pt catalytic surface. The proposed controller successfully forces the process from one stationary state to another state.