The prediction of upcoming events in industrial processes has been a long-standing research goal since it enables optimization of manufacturing parameters, planning of equipment maintenance and more importantly prediction and eventually prevention of defects. While existing approaches have accomplished substantial progress, they are mostly limited to processing of one dimensional signals or require parameter tuning to model environmental parameters. In this paper, we propose an alternative approach based on deep neural networks that simulates changes in the 3D structure of a monitored object in a batch based on previous 3D measurements. In particular, we propose an architecture based on 3D Convolutional Neural Networks (3DCNN) in order to model the geometric variations in manufacturing parameters and predict upcoming events related to sub-optimal performance. We validate our framework on a microelectronics use-case using the recently published PCB scans dataset where we simulate changes on the shape and volume of glue deposited on an Liquid Crystal Polymer (LCP) substrate before the attachment of integrated circuits (IC). Experimental evaluation examines the impact of different choices in the cost function during training and shows that the proposed method can be efficiently used for defect prediction.