Additive manufacturing processes are recent and lack standardized methods to characterize the mechanical properties of the printed material. Sample preparations in the literature consist in the direct printing of specimens, which induces uncontrolled interactions between printing conditions of the specimens and material properties. This study aims to develop a method for the specimen preparation to characterize the behavior of materials manufactured by material extrusion additive manufacturing. The proposed method consists in preparing printed plates from polyethylene terephthalate glycol-modified filament into a unique design before machining out specimens at different orientation angles. A comparison to directly printed specimens at the same orientation angles is performed to confront the proposed method to a commonly used one in the literature, and to understand the cause of discrepancies and the lack of predictiveness in additive manufacturing. The prepared specimens are characterized by X-ray tomography and tensile tests to assess process-structure-property relationships. The analysis highlights the structure heterogeneity of the as-printed specimen compared to the machined one, which influences the mechanical properties of the specimen. The new hybrid additive-subtractive preparation method for the specimen limits the superimposed thermo-kinetic effects caused by changes in deposition strategy, including coalescence and flow instability, and allows to measure effective mechanical properties based on a homogenized multiscale structure that is more representative of large parts. In addition, machining smooths the surface without thermal alterations, which leads to more accurate mechanical testing regarding cross-sectional area measurement, crack initiation and fracture mode. The proposed method is thought to standardize the preparation of additively manufactured materials based on extrusion to ease comparison between studies, to help the qualification of technical and industrial parts, and to measure intrinsic material’s properties based on a controlled microstructure for understanding of the process-related behavior and properties of material.