3D plotting by micro-extrusion is a promising layer-wise fabrication method for the production of scaffolds in thermoplastic polymers. It is a solvent-free direct technique which permits extensive control over geometry and porosity. This paper highlights the complications that arise when using this technique for the processing of thermally sensitive polymers. It has been noted that the material is subject to extensive thermal load during processing, which may result in degradation by chain scission. This negatively affects scaffold (mechanical) properties as well as predictability and repeatability of the fabrication technique. A rationale is offered as to the main causes of this thermally induced degradation during processing and tentative ideas towards a solution are equally put forward.