In this paper, a pilot transmission scheme and a robust self-interference aware relay transceive filter for multipair two-way relaying are introduced. The bidirectional pairwise communications of multiple single-antenna nodes are simultaneously performed via an intermediate non-regenerative multi-antenna relay station and a pilot transmission scheme is proposed to obtain channel state information at the relay station and at the nodes. It is assumed that the nodes can use the available channel state information to subtract the back-propagated self-interference and the cases of perfect and imperfect self-interference cancellation are investigated. The relay station performs linear signal processing based on the estimated channels and a robust relay transceive filter approach is introduced which utilizes the fact that the nodes can perform self-interference cancellation. The proposed pilot transmission scheme requires less resources for channel estimation than conventional schemes and the proposed robust filter design increases the achievable sum rate in case of imperfect channel state information.