Cognitive Radio (CR) has been proposed to address the apparent paradox between spectrum scarcity and spectrum underutilization. It requires the use of a reconfigurable architecture to support a wide range of operating modes. In the case of OFDM-based CR, several subcarriers could interfere with licensed (i.e., the primary) users, so there may be a large number of zero-valued input/output points of the IFFT/FFT and the standard FFT algorithms are not efficient in such a situation. In this paper, we discuss how a more appropriate FFT algorithm, transform decomposition, can be mapped onto a reconfigurable baseband processing architecture. Two mapping methods are proposed to meet various user requirements.