How to make a mesh manifold

I tried trim_with_solid method to drill a hole into a 3D model:

igl::copyleft::cgal::trim_with_solid(m_VA, m_FA, m_VB, m_FB, m_V, m_F, m_D, m_J);

But for hollowed 3D models with inner and outer walls, the hole is not closed:

Possible solution

As posted here, a possible solution might be to use CSG operations of:

igl::copyleft::cgal::mesh_boolean

// or

igl::copyleft::cgal::CSGTree

However, the CSG operations need the input meshes to be manifold.

Question

I couldn't figure out if libigl has any tool to make a mesh manifold. Is there such a tool? Is there any other library which might help?