Structured surfaces enhance the functionality of components. Well known is the influence of the surface structure on friction and wear behavior. Beyond this, structured surfaces are widely used for various purposes such as optical, biological or mechanical applications. Therefore, the characterization of structured surfaces and surface features becomes increasingly important. The functionality of a surface can either be tested directly or indirectly. Due to the correlation of geometric surface features and its functionality, an indirect and self-evident way is by measuring the surface topography. To obtain the geometric essentials of these features, they need to be separated from the raw surface data. The standard procedure of decomposing a surface topography is by the use of a Gaussian filter bank, gaining so called scale-limited surfaces. This procedure shows drawbacks when characterizing structured surfaces by introducing distortions to the feature boundaries. To overcome these limitations, this work proposes the use of an automatic nonlinear anisotropic diffusion filter as an initial step to separate the features from the residual surface topography because of its edge preserving properties. It is shown that the nonlinear anisotropic diffusion serves well the separation of the features and their geometrical characterization.