Femtosecond (fs) laser-thin film interaction is one of the most practical methods for fabricating functional nanostructures. However, the details of the interaction mechanism remain unclear. In this study, we demonstrate an abnormal ablation effect on nanofilms by using a tightly focused single fs laser pulse. After the irradiation of a single Gaussian-shaped femtosecond laser pulse, a molten micro/nanopatch at the irradiated central high-power zone is isolated from the surrounding film. The confined localized threshold effect is proposed as the main mechanism for the phase isolation. With this effect, the high refractive index dielectric Ge2Sb2Te5 crystal nanostructures can be fabricated by directed dewetting of the isolated molten micro/nanopatch on Si substrates. After the laser irradiation, the central isolated liquid through an amorphous GST film is transformed into a crystalline state after resolidification. The isolated central micro/nanopatch size can be controlled by the focused spot size and pulse energy, so that the morphologies (size, geometrical morphology, and distribution) of GST nanostructures can be flexibly modulated. Furthermore, separated solid and liquid phase states detected using spatial-temporal-resolved microscopy validates the crucial role of the confined-localized threshold effect in the dewetting effect based on the separated liquid phase.