The paper describes a software framework for implementing the main stages of the Data Based Mechanistic (DBM) modelling approach to the reduced order emulation (meta-modelling) of large dynamic system computer models, within the Matlab software environment. The framework exploits routines in the CAPTAIN Toolbox to identify and estimate transfer function models that reflect the dominant modes of the dynamic behaviour in the large model. This allows for the ‘nominal emulation’ and validation of the large model for a single, specified set of parameters; as well as ‘stand-alone, full emulation’ based on the construction and validation of hyper-dimensional maps between a user-specified range of large model parameters and the parameters of the associated, low order transfer function models. The software framework uses the multivariable structure constructs available within Matlab™ to form a small library of routines that will become part of the Captain Toolbox. The library is formed around special data structures that facilitate multivariable operations and visualisations which both enhance the efficiency of the emulation modelling analysis and the modeller’s interaction with the process of emulation. The nature of the analysis is illustrated by a topical example concerned with the emulation of the OTIS computer simulation model for the transport and dispersion of solutes in a river system.