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In a Filter Bank based Multicarrier (FBMC) system employed in a highly frequency selective propagation channel each subchannel experiences a multi-tap impulse response (IR). In this contribution we present an efficient method of estimating the IR of the propagation channel experienced by each subchannel, the so-called structured channel estimation. The structured subchannel IR estimation allows us to isolate the propagation channel from the transmit and receive filters. As a consequence the number of parameters to be estimated is reduced as well as the length of the training sequence.