The paper considers the problems of ensuring high accuracy of materials processing processes using low-energy electron beams in the production of elements for quantum microsystems. It is shown that traditional approaches based on the empirical choice of parameters do not always provide the necessary homogeneity and stability of the obtained surfaces, which can lead to the occurrence of microdefects and changes in the functional characteristics of products. Particular emphasis is placed on quantifying the spatial distribution of energy density across the ribbon electron beam’s cross-section, as it critically determines microprocessing accuracy. To address this, a dedicated microprocessor-based information and measurement system has been developed that enables real-time monitoring and control of the electron gun’s operating parameters. The system provides the conversion of the collected current-voltage probe signal, its digital processing, normalization and differentiation, as well as the transmission of data to the computer and to automated control systems via RS-232 and CAN interfaces. The results of experimental studies using KU-1 quartz samples showed an increase in the stability of the irradiation regimes and a decrease in the average height of micro-irregularities of the surface from 40–110 nm to 1.5–6.5 nm. The proposed system creates prerequisites for improving the accuracy, reproducibility and efficiency of technological processes for the formation of high-quality functional elements in the field of micro- and quantum electronics.