The real-time assessment of complex motor skills presents a challenge in fields such as surgical training and rehabilitation. Recent advancements in neuroimaging, particularly functional near-infrared spectroscopy (fNIRS), have enabled objective assessment of such skills with high accuracy. However, these techniques are hindered by extensive preprocessing requirements to extract neural biomarkers. This study presents a novel end-to-end deep learning framework that processes raw fNIRS signals directly, eliminating the need for intermediate preprocessing steps. The model was evaluated on datasets from three distinct bimanual motor tasks--suturing, pattern cutting, and endotracheal intubation (ETI)--using performance metrics derived from both training and retention datasets. It achieved a mean classification accuracy of 93.9% (SD 4.4) and a generalization accuracy of 92.6% (SD 1.9) on unseen skill retention datasets, with a leave-one-subject-out cross-validation yielding an accuracy of 94.1% (SD 3.6). Contralateral prefrontal cortex activations exhibited task-specific discriminative power, while motor cortex activations consistently contributed to accurate classification. The model also demonstrated resilience to neurovascular coupling saturation caused by extended task sessions, maintaining robust performance across trials. Comparative analysis confirms that the end-to-end model performs on par with or surpasses baseline models optimized for fully processed fNIRS data, with statistically similar (p<0.05) or improved prediction accuracies. By eliminating the need for extensive signal preprocessing, this work provides a foundation for real-time, non-invasive assessment of bimanual motor skills in medical training environments, with potential applications in robotics, rehabilitation, and sports.