One of the main challenges for quantum computation is that while the number of gates required to perform a non-trivial quantum computation may be very large, decoherence and errors in realistic quantum architectures limit the number of physical gate operations that can be performed coherently. Therefore, an optimal mapping of the quantum algorithm into the physically available set of operations is of crucial importance. We examine this problem for a measurement-only topological quantum computer based on Majorana zero modes, where gates are performed through sequences of measurements. Such a scheme has been proposed as a practical, scalable approach to process quantum information in an array of topological qubits built using Majorana zero modes. Building on previous work that has shown that multi-qubit Clifford gates can be enacted in a topologically protected fashion in such qubit networks, we discuss methods to obtain the optimal measurement sequence for a given Clifford gate under the constraints imposed by the physical architecture, such as layout and the relative difficulty of implementing different types of measurements. Our methods also provide tools for comparative analysis of different architectures and strategies, given experimental characterizations of particular aspects of the systems under consideration. As a further non-trivial demonstration, we discuss an implementation of the surface code in Majorana-based topological qubits. We use the techniques developed here to obtain an optimized measurement sequence that implements the stabilizer measurements using only fermionic parity measurements on nearest-neighbor topological qubit islands.