In this paper, two general algorithms for the automatic generation of instruction-set extensions are presented. The basic instruction set of a reconfigurable architecture is specialized with new applicationspecific instructions. The paper proposes two methods for the generation of convex multiple input multiple output instructions, under hardware resource constraints, based on a two-step clustering process. Initially, the application is partitioned in single-output instructions of variable size and then, selected clusters are combined in convex multiple output clusters following different policies. Our results on well-known kernels show that the extended Instructions-Set allows to execute applications more efficiently and needing fewer cycles. Our results show that a significant overall application speed-up is achieved even for large kernels (for ADPCM decoder the speed-up is up to x2.2 and for TWOFISH encoder the speedup is up to x5.5).