Understanding the electrical transport properties of nanostructures and metal-nanostructure contacts is important before these can be fabricated into electronic devices. Conductive atomic force microscopy investigations of self-assembled silicon nanostructures are reported here, where the nanostructures are fabricated using electron-beam rapid thermal annealing, a self-assembly process that has been shown to produce field-emission devices using CMOS-compatible technology. Unambiguous correlations between current flow and topography are found, and local current-voltage (IV) spectroscopy measurements are used to determine the ideality factors (1.83-3.20) and barrier heights (0.28-0.49 eV) for the metal-nanostructure contacts.