Since the advent of aligner orthodontics, many aspects of the planning and production processes have evolved. One constant is the fabrication of aligners from thermoforming sheets. The present in vitro study investigates the possibilities of direct 3D printing of aligners with fused filament fabrication. Based on a virtual model, aligners of different thicknesses were created digitally. Activation was planned for 0.4 mm movement of the maxillary left first molar. Aligners were printed using a fused filament fabrication printer with different filaments: three elastic (thermoplastic polyurethane, thermoplastic elastomer and polypropylene) and two stiffer ones (thermoplastic copolymer and polypropylene). Using a special force measurement apparatus with three-axis force and moment sensors, the forces delivered were measured and the aligners were inspected visually. Aligners with a wall thickness greater than 0.9 mm were printed successfully. The surface showed the typical layer structure, and the surface quality was found to differ depending on the material. The forces measured ranged from 0.63 to 1.57 N and moments from 29 to 78 Nmm. Polyethylene terephthalate glycol aligners were too stiff for further investigation. The in vitro measurements indicate that it may be possible to generate biologically effective forces for tooth movement with fused filament fabrication 3D printed aligners. The results may be a starting point for further research on the application of printing elastomers in orthodontics.