Since FPGAs are inherently reconfigurable, making FPGA designs generic does not reduce chip cost, as is the case for ASICs. However, designing and mapping lots of specialized FPGA designs introduces an extra EDA cost. We describe a two staged fully automatic FPGA tool flow that efficiently maps a generic HDL design to multiple specialized FPGA configurations. The mapping is fast enough to be executed on-line in dynamically reconfigurable systems. In this paper we focus on TROUTE, the routing algorithm used in our tool flow. We used TROUTE to implement reconfigurable Multistage Interconnection Networks and show huge improvements in area, speed and mapping time compared to conventional non-reconfigurable implementations.