Most common focusing techniques for Synthetic Aperture Radar (SAR) Tomography (TomoSAR), e.g. Matched Spatial Filtering and Capon, make use of the conventional sample covariance matrix, obtained from a finite number of observations. Yet, structured covariance matrix estimates can be employed in lieu of the sample covariance matrix. Accordingly, our simulation study shows that Capon’s performance improves with the use of structured covariance matrices. These are obtained with the Subspace Fitting approach, properly adapted to TomoSAR. Numerical comparisons between structure and unstructured covariance matrices are presented.