In recent years, an Ultra Wideband (UWB) system has attracted much attention in short range high speed wireless communications. Meanwhile, the single-carrier transmission with frequency domain equalization (SC-FDE) is also attracting much attention. It is reported that the SC-FDE system obtains an excellent performance as well as orthogonal frequency division multiplexing (OFDM), because the SC-FDE system has the advantage of frequency diversity gain even in strong frequency selective channels. However, in the SC-FDE system, cyclic extension reduces the bandwidth efficiency. To improve the bandwidth efficiency, we proposed UWB-IR and DS-UWB with Frequency-Domain Equalization (FDE) and Cyclic Prefix (CP) reconstruction, and showed that when the channel estimation is ideal, the proposed system achieves the good performance. Both FDE and CP reconstruction use channel gains and thus the performance is expected to depend largely on the channel estimation accuracy. In this paper, we evaluate the effect of imperfect channel estimation on the performance of UWB-IR with MMSE-FDE and CP Reconstruction. We show that CP reconstruction is effective for UWB-IR with MMSE-FDE in the IEEE UWB multipath channels, CM3, CM4.