The automatic generation of instruction set extensions (ISEs) to provide application-specific acceleration for embedded processors has been a productive area of research in recent years. The use of automatic algorithms, however, results in instructions that are radically different from those found in conventional Isas. This has resulted in a gap between the hardware's capabilities and the compiler's ability to exploit them. This paper proposes an innovative high-level compiler pass that uses subgraph isomorphism checking to exploit these complex instructions. Our extended code generator also enables the reuse of Ises designed for one application in another, which may be a newer version of the same application or a different one from the same domain. Operating in a separate pass permits computationally expensive techniques to be applied that are uniquely suited for mapping complex instructions, but unsuitable for conventional instruction selection. We demonstrate that this targeted use of an expensive algorithm effectively controls overall compilation time. The existing, mature, compiler back-end can then handle the remainder of the compilation. Instructions are automatically produced for 179 benchmarks, resulting in a total of 1965 unique instructions. The high-level pass integrated into the open-source Gcc compiler is able to use the instructions produced for each benchmark to obtain an average speed-up of 1.26 for the Encore extensible processor.