Results concerning the controllable ablation of nano-layered thin films (NLTF) by femtosecond laser pulses are presented. Investigated samples were titanium-aluminum bilayers, deposited on a silicon substrate, with the top titanium or aluminum layer of variable thickness on the surface. Irradiation was done in ambient air with single femtosecond laser pulses under standard laboratory conditions. The samples were analyzed by complementary methods of optical and scanning electron microscopy and optical profilometry, exhibiting laser-fluence-dependent ablative removal either of the top layer or the entire bilayer or even partial ablation of the underlying silicon substrate. The removal (spallation) threshold fluences for the topmost layer are scalable versus its thickness almost irrespectively of its material, being rather selective for the Ti-coated samples and much less selective for the Al-coated samples. The removal of the entire bilayers was found to be strongly influenced by electronic properties of the underlying metallic layer, dictating the NLTF-Si adhesion, heat conduction, and capacity in the NLTFs toward the NLTF-Si interface and beyond, as well as by their thermophysical characteristics, e.g., almost twice higher melting temperature and enthalpy for Ti. As a result, precise fs-laser machining of the entire NLTFs is pronounced and selective for the samples with the fusible Al at the low-adhesion Al-Si interfaces, compared with the incomplete NLTF removal from the high-adhesion and refractory Ti-Si interfaces.