Additive manufacturing is increasingly adopted for the industrial production of small series of functional components, particularly in thermoplastic strand extrusion processes such as Fused Filament Fabrication. This transition relies on technological advances addressing key process limitations, including dimensional instability, weak interlayer bonding, extrusion defects, moisture sensitivity, and insufficient melting. Process monitoring therefore focuses on early defect detection to minimize failed builds and costs, while ultimately enabling process optimization and adaptive control to mitigate defects during fabrication. For this purpose, a data processing pipeline for monitoring Optical Coherence Tomography images acquired in Fused Filament Fabrication is introduced. Convolutional neural networks are used for the automatic classification of tomographic cross-sections. A dataset of tomographic images passes semi-automatic labeling, preprocessing, model training and evaluation. A sliding window detects outlier regions in the tomographic cross-sections, while masks suppress peripheral noise, enabling label generation based on outlier ratios. Data are split into training, validation, and test sets using block-based partitioning to limit leakage. The classification model employs a ResNet-V2 architecture with BottleneckV2 modules. Hyperparameters are optimized, with N = 2, K = 2, dropout 0.5, and learning rate 0.001 yielding best performance. The model achieves 0.9446 accuracy and outperforms EfficientNet-B0 and VGG16 in accuracy and efficiency.