The magnetoresistance of suspended semiconductor nanostructures with a two-dimensional electron gas structured by periodic square antidot lattices is studied. It is shown that the ballistic regime of electron transport is retained after detaching the sample from the substrate. Direct comparative analysis of commensurability oscillations of magnetoresistance and their temperature dependences in samples before and after suspension is performed. It is found that the temperature dependences are almost identical for non-suspended and suspended samples, whereas significant differences are observed in the nonlinear regime, caused by direct current passage. Commensurability oscillations in the suspended samples are more stable with respect to exposure to direct current, which can be presumably explained by electron–electron interaction enhancement after detaching nanostructures from the high-permittivity substrate.