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Fused deposition modeling (FDM) is one of the widely used additive manufacturing (AM) processes but shares major shortcomings typical due to its layer-by-layer fabrication. These challenges (poor surface finishes, presence of pores, inconsistent mechanical properties, etc.) have been attributed to FDM input process parameters, machine parameters, and material properties. Deep learning, a type of machine learning algorithm has proven to help reveal complex and nonlinear input-output relationships without the need for the underlying physics. This research explores the power of multilayer perceptron deep learning algorithm to create a prediction model for critical input process parameters (layer thickness, extrusion temperature, build temperature, build orientation, and print speed) to predict three functional output parameters (dimension accuracy, porosity, and tensile strength) of FDM printed part. A fractional factorial design of experiment was performed and replicated three times per run (n=3). The number of neurons for the hidden layers, learning rate, and epoch were varied. The computational run time, loss function, and root mean square error (RMSE) were used to select the best prediction model for each FDM output parameter. The findings of this work are being extended to online monitoring and real-time control of the AM process enabling an AM digital twin.