The paper focused on a topic related to the possibilities of using wavelet analysis to evaluate the changes in the geometrical structures of the surfaces arising during the honing process with whetstones with variable granularity. The cylinder liners of the combustion engine are machined elements. The basics of the wavelet analysis and the differences between filtering with standardized filters (e.g., Gauss filter), Fourier analysis, and the analysis of the results obtained when measuring the surface roughness with other wavelets were described. Trials of honing four cylinder liners were carried out. Roughness measurements of 3D spatial structures of the prepared liners were made. The principle of selecting wavelets for roughness assessment of structures with cross-hatch pattern was described. Roughness structures generated on the honed surfaces of cylinder liners were assessed using Gaussian filtration and Morlet, Daubechies Db6, and Mexican hat wavelets. In order to demonstrate the differences generated when the Gaussian filtration and selected wavelets were used on surface structures, the surfaces obtained with the use of these filtering tools were subtracted from each other, which allowed obtaining information about the changes occurring on the assessed surfaces, which were generated after the use of various filtering tools. For the assessed surfaces, during the subtraction operation, the mean square error was calculated, informing about the degree of similarity of both compared surfaces. The result of the work carried out is the creation of basic recommendations for the selection of wavelets when assessing honed surfaces with different degrees of regularity of the traces generated on them.