Three‐dimensional (3D) printing processes are nowadays leading the charge in transforming traditional art, engineering, and manufacturing processes. In this study, the structural and thermal behavior of commercially available filaments composed of synthetic poly(acrylonitrile‐co‐butadiene‐co‐styrene) thermoplastic as well as poly(lactic acid) and poly(lactic acid)/polyhydroxyalcanoate reinforced with bamboo (Bambusa sp.) wood flour composite biothermoplastics were assessed by differential scanning calorimetry and infrared spectroscopy, aiming to understand the modifications that occur at the molecular level during their 3D printing. It has been determined that the biothermoplastic materials undergo both molecular reorientations related to tacticity increase and crystallinity decrease when submitted to 3D printing extrusion, while the synthetic thermoplastic undergoes crosslinking due to its butadiene component. All of the studied materials present good water stability (with water uptake values between 0.8% and 24%), and the water absorption follows a pseudo‐Fickian mechanism. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019.