A multi-mode circuit implements the functionality of a limited number of circuits, called modes, of which at any given time only one needs to be realised. Using run-time reconfiguration of an FPGA, all the modes can be implemented on the same reconfigurable region, requiring only an area that can contain the biggest mode. Typically, conventional run-time reconfiguration techniques generate a configuration for every mode separately. To switch between modes the complete reconfigurable region is rewritten, which often leads to very long reconfiguration times. In this paper we present a novel, fully automated tool flow that exploits similarities between the modes and uses Dynamic Circuit Specialization to drastically reduce reconfiguration time. Experimental results show that the number of bits that is rewritten in the configuration memory reduces with a factor from 4.6X to 5.1X without significant performance penalties.