Yoctolitre-sized vessels (1 yL = 10–24 L) defined by encompassing porphyrin islands by rigid molecular monolayers of diamido bolaamphiphiles (with different characteristics) on smooth surfaces—the so-called yoctowells—have the ability to store (house) molecules in ways reminiscent of a molecular container. Such containers fill by kinetic or thermodynamic trapping processes allowing in some instances for the sorting and spatial positioning of molecular entities within the container. In this Emerging Area we describe the usefulness and versatility of yoctowells as the basis for modeling biological systems with a view to addressing some of the challenges in chemistry, molecular biology and biochemistry.