Motivated by biophysical applications, we consider a free boundary problem for a thin elastic filament immersed in 3D Stokes flow. The 3D fluid is coupled to the quasi-1D filament dynamics via a novel type of angle-averaged Neumann-to-Dirichlet operator. Much of the difficulty in the analysis lies in understanding this operator. We show that the principal part of this NtD map is the corresponding operator about a straight, periodic filament, for which we derive an explicit symbol. It is then possible to establish local well-posedness for an immersed filament evolving via a simple elasticity law. This establishes a mathematical foundation for the myriad computational results based on slender body approximations for thin immersed elastic structures.