Many techniques for high-resolution surface analysis of semiconductors are known, such as optical-, X-ray-, transmission electron microscopy etc. However, atomic-force microscopy and scanning electron microscopy are generally used. In this article, basic principles of scanning electron and atomic-force microscopy are considered. This article shows advantages and disadvantages of each technique. These techniques can be used for quality assessment of semiconductors wafers and structures at different stages of production such as incoming inspection, interoperation inspection and functional control. For AFM study we used “tapping mode” which is well suited for epitaxial structures. SEM images were obtained in secondary electrons imaging mode. These two techniques were compared with respect to the following factors: surface morphology, working environment and the determination of composition. Specific defects for each semiconductor structure and substrates for epitaxy were studied in detail. One of the main advantages of AFM is 3D imaging of the surface together with a “true” vertical resolution less than 0.1 nm. On the contrary, lateral resolution in SEM is better. AFM works under atmospheric environmental conditions that exclude sample preparation. SEM requires vacuum conditions, but at the same time, this “disadvantage” helps to realize its excellent analytical potential. The applicability of these methods for surface morphology investigations of semiconductors such as Ge, MCT, InSb, AlGaN, InGaAs is shown. These materials are commonly used for IR imaging systems in military and civil applications, and their quality is very important. In summary, we conclude that both techniques complement each other. In a modern laboratory it is better to use these techniques side-by-side to achieve satisfactory results.