Liquid nanofilms are ubiquitous in nature and technology, and their equilibrium and out-of-equilibrium dynamics are key to a multitude of phenomena and processes. We numerically study the evolution and rupture of viscous nanometric films, incorporating the effects of surface tension, van der waals forces, thermal fluctuations and viscous shear. We show that thermal fluctuations create perturbations that can trigger film rupture, but they do not significantly affect the growth rate of the perturbations. The film rupture time can be predicted from a linear stability analysis of the governing thin film equation, by considering the most unstable wavelength and the thermal roughness. Furthermore, applying a sufficiently large unidirectional shear can stabilise large perturbations, creating a finite-amplitude travelling wave instead of film rupture. In three dimensions, unidirectional shear does not inhibit rupture, as perturbations are not suppressed in the direction perpendicular to the applied shear. However, if the direction of shear varies in time, the growth of large perturbations is prevented in all directions, and rupture can be impeded.