In this paper, a novel method for the modeling and characterization of surface structures is presented. The method is based on the nonparametric statistical modeling of the surface structure, represented as a two dimensional field. Using a sample of a surface structure in question, the model reproduces the structure of the surface and estimates the corresponding machining parameters. The applicability of the method is demonstrated on the modeling and characterization of the functional surfaces generated by intentionally invoked chatter during the milling process. Based on the model of the generated surface structures, the corresponding diameter of the toroidal cutter and spindle speed are estimated using the surface structure data as the input for the model.