It is challenging to selectively remove a thin film with a high melting temperature from an underlying one with a low melting temperature where precise stops at layer interfaces are required. In this study, an ultrashort laser pulse is used to cleanly ablate a 40 nm thin molybdenum layer from an aluminium thin film in a commercially relevant heterostructure. We observe clean delamination of molybdenum from aluminium. We observe that columnar nanostructures in Mo are generated well below the damage threshold fluence. Both delamination and nanostructure formation are considered in terms of electromechanical forces. At low fluence, only selective removal of the very near surface of the Mo thin film was observed. At higher fluences, ablation of the Mo film occurred without melting of the underlying Al layer. Our computational results confirm the important role of thermionic electron emission and near surface electron-phonon coupling in nanostructure generation. We introduce a thermal boundary resistance effect in the heat diffusion by electrons to more accurately describe the release of the Mo from the Al layer. The comparison of experimental and simulation results confirms that electromechanical stresses can be an important mechanism in selective thin film ablation.