The practical deployment of learning-based autonomous systems would greatly benefit from tools that flexibly obtain safety guarantees in the form of certificate functions from data. While the geometrical properties of such certificate functions are well understood, synthesizing them using machine learning techniques still remains a challenge. To mitigate this issue, we propose a diffeomorphic function learning framework where prior structural knowledge of the desired output is encoded in the geometry of a simple surrogate function, which is subsequently augmented through an expressive, topology-preserving state-space transformation. Thereby, we achieve an indirect function approximation framework that is guaranteed to remain in the desired hypothesis space. To this end, we introduce a novel approach to construct diffeomorphic maps based on RBF networks, which facilitate precise, local transformations around data. Finally, we demonstrate our approach by learning diffeomorphic Lyapunov functions from real-world data and apply our method to different attractor systems.