A coherence scanning tomographic imaging system with an innovative signal correction method is presented for a critical dimension (CD) measurement of thin film transistor liquid crystal display patterns having multiple focus positions within a single field of view. To facilitate the analyzing of coherence signals, a simulation model based on fast Fourier transform method is proposed, and its simulated result is compared with the coherence signals from the actual experiments. The comparison shows that the majority of frequency characteristics from simulation modeling results are matched with the experimental results. However, in many edge regions, discrepancies in frequency characteristics between the two results are observed. For the interpretation of signals, those are different from the simulation modelling, in that the intensity of its pixels has been corrected by an innovatively proposed connected neighborhoods window method with multiple window sizes. By using this combination of tomographic imaging and edge correction methods, the repeatability of the CD measurement of multiple focus position samples is significantly enhanced compared to the results with a plain two-dimensional optics. The proposed method is also compared with the autofocus methods including gradient magnitude method and frequency domain method and other tomographic imaging methods, including the phase shift method and the Hilbert transform method to show the advantages in the processing time.