Recent advances in experimental techniques emphasize the usefulness of multiple scanning probe techniques when analyzing nanoscale samples. Here, we analyze theoretically dual-probe setups with probe separations in the nanometer range, i.e., in a regime where quantum coherence effects can be observed at low temperatures. In a dual-probe setup the electrons are injected at one probe and collected at the other. The measured conductance reflects the local transport properties on the nanoscale, thereby yielding information complementary to that obtained with a standard one-probe setup (the local density of states). In this work we develop a real-space Green's function method to compute the conductance. This requires an extension of the standard calculation schemes, which typically address a finite sample between the probes. In contrast, the developed method makes no assumption of the sample size (e.g., an extended graphene sheet). Applying this method, we study the transport anisotropies in pristine graphene sheets, and analyze the spectroscopic fingerprints arising from quantum interference around single-site defects, such as vacancies and adatoms. Furthermore, we demonstrate that the dual-probe setup is a useful tool for characterizing the electronic transport properties of extended defects or designed nanostructures. In particular, we show that nanoscale perforations, or antidots, in a graphene sheet display Fano-type resonances with a strong dependence on the edge geometry of the perforation.