Material Extrusion (MEX) technology, a prominent process in the field of additive manufacturing (AM), has witnessed significant growth in recent years. The continuous quest for enhanced material properties and refined surface quality has led to the exploration of post-processing techniques. In this study, we delve into the ironing process as a vital processing step, focusing on the optimization of its parameters through the application of Design of Experiments (DoE), specifically the Box–Behnken Design (BBD). Through a systematic examination of ironing process parameters, we identified optimal conditions that resulted in a substantial reduction in surface roughness (Ra) by approximately 69%. Moreover, the integration of optimized ironing process parameters led to remarkable improvements in mechanical properties. For instance, the Ultimate Tensile Strength (UTS) saw a substantial improvement of approximately 29%, while the compressive strength (CS) showed an increase of about 25%. The flexural strength (FS) witnessed a notable enhancement of around 35%, and the impact strength (IS) experienced a significant boost of about 162%. The introduction of ironing minimizes voids, enhances layer bonding, and reduces surface irregularities, resulting in components that not only exhibit exceptional mechanical performance but also possess refined aesthetics. This research sheds light on the transformative potential of precision experimentation, post-processing techniques, and statistical methodologies in advancing Material Extrusion technology. The findings offer practical implications for industries requiring high-performance components with structural integrity and aesthetic appeal.