We study the magnetotransport properties of patterned 3D topological insulator nanostructures with several leads, such as kinks or Y-junctions, near the Dirac point with analytical as well as numerical techniques. The interplay of the nanostructure geometry, the external magnetic field and the spin-momentum locking of the topological surface states lead to a richer magnetoconductance phenomenology as compared to straight nanowires. Similar to straight wires, a quantized conductance with perfect transmission across the nanostructure can be realized across a kink when the input and output channels are pierced by a half-integer magnetic flux quantum. Unlike for straight wires, there is an additional requirement depending on the orientation of the external magnetic field. A right-angle kink shows a unique $pi$-periodic magnetoconductance signature as a function of the in-plane angle of the magnetic field. For a Y-junction, the transmission can be perfectly steered to either of the two possible output legs by a proper alignment of the external magnetic field. These magnetotransport signatures offer new ways to explore topological surface states and could be relevant for quantum transport experiments on nanostructures which can be realized with existing fabrication methods.