This paper addresses the problem of relative transfer function (RTF) estimation in the presence of stationary noise. We propose an RTF identification method based on segmental power spectral density (PSD) matrix subtraction. First multiple channel microphone signals are divided into segments corresponding to speech-plus-noise activity and noise-only. Then, the subtraction of two segmental PSD matrices leads to an almost noise-free PSD matrix by reducing the stationary noise component and preserving non-stationary speech component. This noise-free PSD matrix is used for single speaker RTF identification by eigenvalue decomposition. Experiments are performed in the context of sound source localization to evaluate the efficiency of the proposed method.