In this paper we study the problem of deciding the existence of a subgraph epimorphism between two graphs. Our interest in this variant of graph matching problem stems from the study of model reductions in systems biology, where large systems of biochemical reactions can be naturally represented by bipartite digraphs of species and reactions. In this setting, model reduction can be formalized as the existence of a sequence of vertex deletion and merge operations that transforms a first reaction graph into a second graph. This problem is in turn equivalent to the existence of a subgraph (corresponding to delete operations) epimorphism (i.e. surjective homomorphism, corresponding to merge operations) from the first graph to the second. In this paper, we study theoretical properties of subgraph epimorphisms in general directed graphs. We first characterize subgraph epimorphisms (SEPI), subgraph isomorphisms (SISO) and graph epimorphisms (EPI) in terms of graph transformation operations. Then we study the graph distance measures induced by these transformations. We show that they define metrics on graphs and compare them. On the algorithmic side, we show that the SEPI existence problem is NP-complete by reduction of SAT, and present a constraint satisfaction algorithm that has been successfully used to solve practical SEPI problems on a large benchmark of reaction graphs from systems biology.