Model-Based Development has become an industry wide standard paradigm. As an open source alternative, Scilab/Xcos is being widely employed as a hybrid dynamic systems modeling tool. With the increasing efficiency in implementation using graphical model development and code generation, the modeling and simulation community is struggling with assuring quality as well as maintainability and extendibility. Refactoring is defined as an evolutionary modernization activity where, most of the time, the structure of the artifact is changed to alter its quality characteristics, while keeping its behavior unchanged. It has been widely established as a technique for textual programming languages to improve the code structure and quality. While refactoring is also regarded as one of the key practices of model engineering, the methodologies and approaches for model refactoring are still under development. Architecture-Driven Modernization (ADM) has been introduced by the software engineering community as a model-based approach to software modernization, in which the implicit information that lies in software artifacts is extracted to models and model transformations are applied for modernization tasks. Regarding refactoring as a low level modernization task, the practices from ADM are adaptable. Accordingly, this paper proposes a model-based approach for model refactoring in order to come up with more efficient and effective model refactoring methodology that is accessible and extendable by modelers. Like other graphical modeling tools, Scilab/Xcos also possesses a formalized model specification conforming to its implicit metamodel. Rather than proposing another metamodel for knowledge extraction, this pragmatic approach proposes to conduct in place model-to-model transformations for refactoring employing the Scilab/Xcos model specification. To construct a structured model-based approach, the implicit Scilab/Xcos metamodel is explicitly presented utilizing ECORE as a meta-metamodel. Then a practical model transformation approach is established based on Scilab scripting. A Scilab toolset is provided to the modeler for in-place model-to-model transformations. Using a sample case study, it is demonstrated that proposed model transformation functions in Scilab provide a valuable refactoring tool.