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It has been predicted that a processor's caches could occupy as much as 90% of chip area for technology nodes from the current. In this paper, we study the use of multi-level spin-transfer torque RAM (STT-RAM) cells in the design of processor caches. Compared to the traditional SRAM caches, a multi-level cell (MLC) STT-RAM cache design is denser, fast, and consumes less energy. However, a number of critical issues remains to be solved before MLC STT-RAM technology can be deployed in processor caches. In this paper, we shall offer solutions to the issue of bit encoding as well as tackle the write endurance problem. The latter has been neglected in previous works on STT-RAM caches. We propose a set remapping scheme that can potentially prolong the lifetime of a MLC STT-RAM cache by 80× on average. Furthermore, a method for recovering the performance that may be lost in some applications due to set remapping is introduced.