We present a new approach to designing multi-mode FIR filters in FPGAs based on partitioning a design into shared, mode-independent blocks and reconfigurable, modespecific regions. We also provide a theoretical formulation for finding an optimal sequence of modes that minimizes a joint cost function related to area and reconfiguration overhead. Our results show that for a group of template matching filters, appropriate mode sequencing can reduce area by up to 15% and reconfiguration overhead by as much as 26%.