Precise nanofabrication represents a critical challenge to developing semiconductor quantum-dot qubits for practical quantum computation. Here, we design and train a convolutional neural network to interpret in-line scanning electron micrographs and quantify qualitative features affecting device functionality. The high-throughput strategy is exemplified by optimizing a model lithographic process within a five-dimensional design space and by demonstrating a new approach to address lithographic proximity effects. The present results emphasize the benefits of machine learning for developing robust processes, shortening development cycles, and enforcing quality control during qubit fabrication.