Permalloy disc structures in magnetic vortex state constitute a promising new type of magnetic nanoparticles for biomedical applications. They present high saturation magnetisation and lack of remanence, which ease the remote manipulation of the particles by magnetic fields and avoid the problem of agglomeration, respectively. Importantly, they are also endowed with the capability of low-frequency magneto-mechanical actuation. This effect has already been shown to produce cancer cell destruction using functionalized discs, about 1 μm in diameter, attached to the cell membrane. Here, Permalloy nanodiscs down to 60 nm in diameter are obtained by hole-mask colloidal lithography, which is proved to be a cost-effective method for the uniform patterning of large substrate areas, with a high production yield of nanostructures. The characterisation of the magnetic behaviour of the nanodiscs, complemented with micromagnetic simulations, confirms that they present a very well defined magnetic vortex configuration, unprecedented, to our knowledge, for nanostructures of this size prepared by a high-yield method. The successful detachment of the gold-covered nanodiscs from the substrate is also demonstrated by the use of sacrificial layers.