Fully Dense Freeform Fabrication uses an adaptive layering method for predefined sheets and uses slices cut by a water cutter or laser cutter machine for manufacturing functional parts through smart layer alignment, adjustable compression system, and compatible bonding materials. Under pressure and heat, layers are attached and form a 3D prototype. This paper presents an automated alignment mechanism and compression bonding method that is functional for a variety of complex parts. The alignment system makes a nest setting by using five linear actuators and the compression system is using an array of uneven pins that are locked by sliding surfaces.