In this paper a problem domain and system modelling formalization approach is shown in context of enterprise data synchronization system development case study. Formalization approach is based on topology borrowed from topological functioning model (TFM). TFM uses mathematical foundations that holistically represent complete functionality of the problem and application domains. By applying the proposed topological modelling approach in software development process we aim to enable computation independent model creation in a formal way and to enable transformation from it to platform independent model. Besides that a traceability can be established between problem domain model, solution domain model (or models) and the software code.