Parameteristion in non manifold meshes

Question

I have a mesh with non manifold edges and vertices present in it and have to parameterise this mesh. Now i have been using isoparameterisation in Meshlab to achieve the same. But due to the presence on non manifold edges the paramterisation does not work. I cannot remove all the non manifold edges as it creates a multi component mesh. Iso Paramterisation in meshlab does not work for multi component meshes. Can any one suggest me which technique/ software should I use to achieve parameterisation in such a mesh ? Thanks