The progressive industrial adoption of Model-Driven Engineering (MDE) is fostering the development of large tool ecosystems like the Eclipse Modeling project. These tools are built on top of a set of base technologies that have been primarily designed for small-scale scenarios, where models are manually developed. In particular, efficient runtime manipulation for large-scale models is an under-studied problem and this is hampering the application of MDE to several industrial scenarios.In this paper we introduce and evaluate a map-based persistence model for MDE tools. We use this model to build a transparent persistence layer for modeling tools, on top of a map-based database engine. The layer can be plugged into the Eclipse Modeling Framework, lowering execution times and memory consumption levels of other existing approaches. Empirical tests are performed based on a typical industrial scenario, model-driven reverse engineering, where very large software models originate from the analysis of massive code bases. The layer is freely distributed and can be immediately used for enhancing the scalability of any existing Eclipse Modeling tool.