The tool indexing problem (TIP) is the problem of allocating cutting tools to different slots in a tool magazine of Computer Numerically Controlled machine to reduce the processing time of jobs on the machine. This is one of the mostly encountered optimization problems in manufacturing systems. In TIP, the number of tools used by the machine is at most the number of slots available in the tool magazine. In this article, a customized harmony search (HS) algorithm, which utilizes a harmony refinement strategy for faster convergence, is presented to solve TIP. The harmony refinement method also helps to avoid getting stuck into local optima. The performance of the proposed method is tested on 27 instances taken from the literature and out of these it is found to improve the best known solutions for 16 instances. For the remaining instances, it gives the same results as found in the literature. Moreover, the performance of the proposed algorithm is tested on newly adapted 41 instances and for some of these instances the results obtained using the proposed algorithm are compared with that obtained using CPLEX.