X-ray fluorescence analysis (XRF) is a widespread and preferred method for a variety of analytical applications. Among other things, due to its non-invasiveness and non-destructiveness, it is an excellent method for exploring the valuable objects of our cultural heritage. At the same time, however, the fact that it uses relatively low energy X-rays brings some limitations and problems in interpreting the measurement results, especially if objects with inhomogeneous structure are investigated. The depth in the examined material from which characteristic X-rays are detected is in the order of tens to hundreds of μm, depending on the measured element and composition and density of the material. During the development and use of XRF, several procedures have been developed to estimate whether the examined element is distributed homogeneously in the measured layer or has a depth uneven distribution. The least difficult is the measurement under different angles of excitation and excited radiation impact and emission. More sophisticated options are the simultaneous use of Kα and Kβ lines, or K and L lines. The most comprehensive information can be obtained in the confocal arrangement of the spectrometer, where both incident and emitted radiation are narrowly collimated, and the intersection of the two collimated beams is gradually moved under the surface of the object under investigation. The aim of this review paper is to summarize possible procedures for identifying the inhomogeneous structure of the material and test them in the model case of the thickness standards for the copper layer on the steel.