Terahertz time-of-flight tomography is employed to characterize the individual layers in a multilayer coating on steel substrates. The multilayers, containing up to three layers, consist first of a cataphoretic layer, sealer, and varnish progressing upward from the steel substrate. The individual layer thicknesses were reconstructed from the experimental data using autoregressive spectral extrapolation based on the modified covariance method (AR/MCM), which extrapolates the frequency components of the transfer function into the low signal-to-noise-ratio (SNR) regions from the high SNR regions. Due to the high sensitivity of AR/MCM to the presence of noises, wavelet denoising, in some cases, was needed to precondition the data prior to application of AR/MCM. The method is verified numerically and experimentally, showing that it can reconstruct individual layers in the 10-μm range, and good agreement is found between the thicknesses of individual layers extracted by AR/MCM and characterized by eddy-current measurements.