In this paper, we first overview the least square (LS) space-time joint channel estimation in filtered multi-tone (FMT) system in multi-input multi-output (MIMO) system. Then the design of pilots aiming at mitigating the inter-cell interference in MIMO FMT systems is addressed. It is shown that if the pilots which result in a zero variation coefficient of the estimation error are used, the better performance on system level was obtained. The properties of these pilots are described, and the simulation results are presented.