This work presents a new multimodal system for remote attention level estimation based on multimodal face analysis. Our multimodal approach uses different parameters and signals obtained from the behavior and physiological processes that have been related to modeling cognitive load such as faces gestures (e.g., blink rate, facial actions units) and user actions (e.g., head pose, distance to the camera). The multimodal system uses the following modules based on Convolutional Neural Networks (CNNs): Eye blink detection, head pose estimation, facial landmark detection, and facial expression features. First, we individually evaluate the proposed modules in the task of estimating the student's attention level captured during online e-learning sessions. For that we trained binary classifiers (high or low attention) based on Support Vector Machines (SVM) for each module. Secondly, we find out to what extent multimodal score level fusion improves the attention level estimation. The mEBAL database is used in the experimental framework, a public multi-modal database for attention level estimation obtained in an e-learning environment that contains data from 38 users while conducting several e-learning tasks of variable difficulty (creating changes in student cognitive loads).