In topology, a torus remains invariant under certain nontrivial transformations known as modular transformations. In the context of topologically ordered quantum states of matter supported on a torus geometry in real space, these transformations encode the braiding statistics and fusion rules of emergent anyonic excitations and thus serve as a diagnostic of topological order. Moreover, modular transformations of higher genus surfaces, e.g., a torus with multiple handles, can enhance the computational power of a topological state, in many cases providing a universal fault-tolerant set of gates for quantum computation. However, due to the intrusive nature of modular transformations, which abstractly involve global operations, physical implementations of them in local systems have remained elusive. Here, we show that by engineering an effectively folded manifold corresponding to a multilayer topological system, modular transformations can be applied in a single shot by independent local unitaries, providing a novel class of transversal logical gates for fault-tolerant quantum computation. Specifically, we demonstrate that multilayer topological states with appropriate boundary conditions and twist defects allow modular transformations to be effectively implemented by a finite sequence of local SWAP gates between the layers. We further provide methods to directly measure the modular matrices, and thus the fractional statistics of anyonic excitations, providing a novel way to directly measure topological order. A more general theory of transversal gates and the deep connection to anyon symmetry transformation and symmetry-enriched topological orders are also discussed.