This article is devoted to the development of a computer system for studying the leukemia based on the analysis of the surface relief of lymphocytes in three-dimensional images of blood cells. The implementation of the algorithm in the framework of this development is to determine the morphometric parameters of the surface structures of lymphocytes, the determination of which is an important factor in the diagnosis of blood disease. Recently, relevant to solving this issue is the study of the surface relief of lymphocytes in three-dimensional images of blood cells obtained using atomic force microscopy technologies. The results of the initial scanning through a microscope are mathematically processed using specially developed software for this diagnostic equipment. However, existing software products that come with the hardware they do not provide an opportunity to search for globular depressions and protrusions characteristic of the surface of lymphocytes, the morphometric parameters of which dynamically change during pathology. In this regard, there is a need for the development of a computer system, able to automate the process of research and analysis of the surface relief of blood cells. An algorithm has been developed for its implementation, with the help of which it is possible to automatically search for all globular depressions and protrusions present on it on a three-dimensional image of the cell surface of lymphocytes obtained through a microscope, from microscopic to visually detectable, as well as their geometric parameters.