The analysis of 2D scattering maps generated in scatterometry experiments for detection and classification of nanoparticles on surfaces is a cumbersome and slow process. Recently, deep learning techniques have been adopted to avoid manual feature extraction and classification in many research and application areas, including optics. In the present work, we collected experimental datasets of nanoparticles deposited on wafers for four different classes of polystyrene particles (with diameters of 40, 50, 60, and 80 nm) plus a background (no particles) class. We trained a convolutional neural network, including its architecture optimization, and achieved 95% accurate results. We compared the performance of this network to an existing method based on line-by-line search and thresholding, demonstrating up to a twofold enhanced performance in particle classification. The network is extended by a supervisor layer that can reject up to 80% of the fooling images at the cost of rejecting only 10% of original data. The developed Python and PyTorch codes, as well as dataset, are available online.