It has been proposed that localized zero-energy Majorana states can be realized in a two-dimensional network of quasi-one-dimensional semiconductor wires that are proximity coupled to a bulk superconductor. The wires should have strong spin-orbit coupling with appropriate symmetry, and their electrons should be partially polarized by a strong Zeeman field. Then, if the Fermi level is in an appropriate range, the wire can be in a topological superconducting phase, with Majorana states that occur at wire ends and at Y junctions, where three topological superconductor segments may be joined. Here we generalize these ideas to consider a three-dimensional network. The positions of Majorana states can be manipulated, and their non-Abelian properties made visible, by using external gates to selectively deplete portions of the network or by physically connecting and redividing wire segments. Majorana states can also be manipulated by reorientations of the Zeeman field on a wire segment, by physically rotating the wire about almost any axis, or by evolution of the phase of the order parameter in the proximity-coupled superconductor. We show how to keep track of sign changes in the zero-energy Hilbert space during adiabatic manipulations by monitoring the evolution of each Majorana state separately, rather than keeping track of the braiding of all possible pairs. This has conceptual advantages in the case of a three-dimensional network, and may be computationally useful even in two dimensions, if large numbers of Majorana sites are involved.