Developments in polymer 3D printing (3DP) technologies have expanded their scope beyond the rapid prototyping space into other high-value markets, including the consumer sector. Processes such as fused filament fabrication (FFF) are capable of quickly producing complex, low-cost components using a wide variety of material types, such as polylactic acid (PLA). However, FFF has seen limited scalability in functional part production partly due to the difficulty of process optimization with its complex parameter space, including material type, filament characteristics, printer conditions, and “slicer” software settings. Therefore, the aim of this study is to establish a multi-step process optimization methodology—from printer calibration to “slicer” setting adjustments to post-processing—to make FFF more accessible across material types, using PLA as a case study. The results showed filament-specific deviations in optimal print conditions, where part dimensions and tensile properties varied depending on the combination of nozzle temperature, print bed conditions, infill settings, and annealing condition. By implementing the filament-specific optimization framework established in this study beyond the scope of PLA, more efficient processing of new materials will be possible for enhanced applicability of FFF in the 3DP field.