One should be able to specify boundary conditions on all external boundaries of any geometry.
For example, look at the “A scattering problem” example in the documentation. It has a Neumann condition at the outer boundary and a Dirichlet condition at the inner boundary (that is formed by the square sub-region).
Boundary conditions on internal boundaries such as boundaries across which material properties or governing equations might change are not required by Finite Element method.
Best Answer
It depends how you generated the mesh:
Alan Weiss
MATLAB mathematical toolbox documentation