Controlling self-assembly is a key issue in many applications such as encapsulation of drugs, micelle separation, and fabrication of nanoporous materials. For providing guidance to control self-assembly, a reliable prognosis of aggregation behavior is indispensable. Molecular thermodynamic models have been developed for different types of soft mesoscale structures formed by aggregating chainlike amphiphilic molecules. Examples include nonionic and ionic copolymer gels swelling in selective solvents, surfactant micellar solutions and amphiphilic membranes. Though rather different in chemical nature and applications, these systems are all characterized by self-assembly into soft mesoscale structures that are sensitive to external conditions or applied stimuli. The models predict a number of thermodynamic and structural characteristics (equilibrium size and stability of different morphologies, equilibrium swelling, elastic properties, solute partitioning, etc.) in terms of several adjustable parameters and molecular characteristics of components. Consideration of nanoscale morphology gives rise to interesting structure-property relations reflected by relatively simple models. New findings help estimate how variations of controllable factors such as pH, salinity and additives affect self-assembly patterns and aggregate properties. Recent advances in the development of molecular thermodynamic aggregation models, factors restricting implementation of these models and trends in the field are discussed. (c) 2015 Society of Chemical Industry