Many advances in the development of nano and microchemical systems have occurred in the last decade. These systems have significant associated identification and control challenges, including high state dimensionality, limitations in real-time measurements and manipulated variables, and significant uncertainties described by non-Gaussian distributions. Some strategies for addressing these challenges are summarized, which include exploiting structure within the stochastic Master equations that describe molecular interactions, manipulating molecular bonds at system boundaries, and manipulating molecules and nanoscale objects through magnetic and electric fields. The strategies are illustrated in a variety of applications that include the estimation of nucleation kinetics of protein and pharmaceutical crystals within fluidic devices, the estimation of concentration fields using DNA-wrapped single-walled carbon nanotube-based sensor arrays, the simultaneous control of nanoscale geometry and electrical activation during thermal annealing in a semiconductor material, and the control of nanostructure formation on surfaces. Promising directions for research and technology development are identified for the next decade. (C) 2012 Elsevier Ltd. All rights reserved.