Donor-based qubits in silicon, manufactured using scanning tunneling microscope (STM) lithography, provide a promising route to realizing full-scale quantum computing architectures. This is due to the precision of donor placement, long coherence times, and scalability of the silicon material platform. The properties of multiatom quantum dot qubits, however, depend on the exact number and location of the donor atoms within the quantum dots. In this work, we develop machine learning techniques that allow accurate and real-time prediction of the donor number at the qubit site during STM patterning. Machine learning image recognition is used to determine the probability distribution of donor numbers at the qubit site directly from STM images during device manufacturing. Models in excess of 90% accuracy are found to be consistently achieved by mitigating overfitting through reduced model complexity, image preprocessing, data augmentation, and examination of the intermediate layers of the convolutional neural networks. The results presented in this paper constitute an important milestone in automating the manufacture of atom-based qubits for computation and sensing applications.