Recently, carbon fiber-reinforced thermoplastics (CFRTPs) have become popular choices in desktop-based additive manufacturing, but there is limited information on their effective usage. In Fused Deposition Modeling (FDM), a structure is created by layers of extruded beads. The degree of bonding between beads, bead orientation, degree of interlayer bonding, type of infill and the type of material, determines overall mechanical performance. The presence of chopped fibers in thermoplastics increases melt viscosity, changes coefficients of thermal expansion, may have layer adhesion issues, and causes increased wear on nozzles, which makes FDM fabrication of thermoplastic composites somewhat different from neat thermoplastics. In the current work, best practices and the effect of annealing and infill patterns on the mechanical performance of FDM-fabricated composite parts were investigated. Materials included commercially available PLA, CF-PLA, ABS, CF-ABS, PETG, and CF-PETG. Two sets of ASTM D638 tensile and ASTM D790 flexural test specimens with 3 different infill patterns and each material were fabricated, one set annealed, and all tested. Anisotropic behavior was observed as a function of infill pattern. As expected, strength and stiffness were higher when the beads were oriented in the direction of the load, even for neat resins. All fiber-filled tensile results showed an increase in stiffness, but surprisingly, not in strength (likely due to very short fiber lengths). Tests of annealed specimens resulted in clear improvements in tensile strength, tensile stiffness and flexural strength for PLA, CF-PLA, and PETG, CF-PETG but a reduction in flexural stiffness. Also, annealing resulted in mixed improvements for ABS and CF-ABS and is only useful in certain infill patterns. This work also establishes ‘Best Practices’ of FDM-type fabrication of thermoplastic composite structures and documents the minimum critical fiber lengths and fiber fractions of several CF-filled FDM filaments.