The paper presents a methodology for evaluating the repeatability of objective positioning in the Focus Variation (FV) technique, using advanced procedures for topographic data extraction and their functional analysis.A measurement scheme is proposed based on statistical analysis of two acquisition types: a reference measurement, in which the objective is not displaced by more than 4 mm, and a sequential measurement, in which each subsequent scan is preceded by a displacement of the objective along a selected axis in the range of 40–80 mm. For both strategies, the scatter of surface topography parameters was determined and used to estimate the focal positioning error of the objective, treated as a component of the FV technique’s uncertainty budget. It was demonstrated that, in the reference configuration, a repeatability of 98.7% was achieved for key functional parameters, whereas in the sequential mode the repeatability was 77.6%, indicating a significant influence of long axial displacements on positioning stability. The practical implications of these differences for the selection of scanning strategies, comparability of results, and the design of control procedures in surface engineering are discussed. The proposed methodology constitutes a universal tool for the validation of FV systems and can be directly used to monitor the condition of the drive system, optics, and reconstruction algorithms, as well as to quantify measurement uncertainty in industrial and research applications.