Fused filament fabrication (FFF) is an extrusion-based process that allows quick and inexpensive part production, practically without any geometric limitations, offering flexibility, promoting reduction in costs and lead-time in an industrial scenario. Being one of the most widespread additive manufacturing techniques, the process has evolved introducing new and advanced materials (e.g. high-performance polymers and composites). Despite its advantages, the process is vastly overlooked due to its high level of anisotropy, poor surface roughness and lack of geometric accuracy caused by the layer thickness. To reduce this effect, a sequence of laborious manual operations can be performed, which may result in time-consuming and inaccurate results. Therefore, efforts have been made towards the development of hybrid manufacturing technologies by combining FFF process and subtractive equipment, aiming to solve these limitations. In this work, two complementary methodologies analysing the behaviour of FFF PA12 and short fibre–reinforced PA12 printed parts when subjected to a subtractive approach are presented. The first experimental plan took into account the final surface roughness (Ra and Rz) via full factorial design of experiments (DOE) and analysis of variance (ANOVA) considering the influence of distinct printing orientations, two types of cutting tools and machining parameters such as, cutting speed, feed and cutting depth. An analysis on tool wear and SEM microscopy to the machined surface was also performed. The second approach was carried out via Taguchi and ANOVA, considering the first experimental approach results. Thus, milling parameters were the focus, evaluating the final material surface roughness, being now monitored the cutting forces and tool wear analysis in order to understand their influence on the final results. It is shown that it is possible to machine PA12-based FFF printed parts without any major problems such as layer delamination. A decrease in Ra, t of 1931% to 0.99 μ m for PA12CF and 2255% for PA12 to 0.96 μ m was achieved, proving the overall machinability of the materials. It was found that PA12 creates higher levels of cutting loads and increased tool wear, thus indicating that short fibre presence improves the material machinability, while parameters such as building orientation do not possess any influence on the final surface roughness.