In this paper, the topography of 6082 aluminium alloy specimens after fatigue bending tests was studied with a comprehensive evaluation of measurement noise caused by vibration. Roughness results were acquired by contactless Focus Variation Microscopy (FVM). Studied data were pre-processed, removing the non-measured points and outliers with regular methods, respectively, and high-frequency noise was considered. The variations in ISO 25178 roughness parameters were studied. Based on the previous studies, it was found that surfaces after fatigue bending tests can be difficult to consider when analyzing the measurement noise in a selected bandwidth. Some advantages of profile data extraction in selected directions, like horizontal, vertical or crack, were found deficient, even in studies by various functions, like autocorrelation, power spectral density, or texture direction ratio. When noise suppression methods depend on the details studied, boundary areas were extracted to compare and highlight the presence of high-frequency data characteristics. The proposed method was validated when contrasting standardised Gaussian or median filtering techniques with the spline filtering approach. A proper filter for the reduction of vibrational noise from the results of FVM topography measurements was suggested based on the proposed procedure. Finally, it was proposed how use the new method for reducing errors caused by high-frequency measurement noise in the surface topography of specimens after fatigue bending tests.