In this paper, we propose a multi-layer precoding scheme to reduce PAPR in MIMO-OFDM systems. Specifically, an outer-layer polyphase precoding matrix P is custom designed using the trellis exploration algorithm that was previously applied to the design of spreading sequences for CDMA systems. The algorithm determines the P matrix that results in the minimum aperiodic autocorrelation (and therefore minimum PAPR) among transmitted OFDM data symbols. Simulation results illustrate that the proposed multi-layer precoding scheme can not only significantly lower the PAPR in a MIMO-OFDM, but also well preserve the performance gains that are obtained by inner-layer precoding.