Surfen dihydrochloride is used in biomedical research to modulate signaling pathways involving heparan sulfate proteoglycans (HSPGs). It blocks the interaction of HSPGs with various growth factors and cytokines, such as fibroblast growth factors (FGFs) and bone morphogenetic proteins (BMPs), making it a valuable tool for studying tissue development, regeneration, and inflammation.

It has been applied in stem cell research to improve the efficiency of directed differentiation by fine-tuning growth factor signaling. Surfen also shows potential in reducing fibrosis in preclinical models by inhibiting profibrotic signaling pathways. Additionally, it is investigated for its role in enhancing drug delivery by modifying the extracellular matrix barrier in tissues. Its ability to influence cellular signaling makes it useful in studies related to cancer progression and neural repair.