Purpose – This paper aims to report a detailed study regarding the influence of process parameters on the morphological/mechanical properties of poly(e-caprolactone) (PCL) scaffolds manufactured by using a novel extrusion-based system that is called BioExtruder. Design/methodology/approach – In this study the authors focused investigations on four parameters, namely the liquefier temperature (LT), screw rotation velocity (SRV), deposition velocity (DV) and slice thickness (ST). Scaffolds were fabricated by employing three different values of each parameter. Through a series of trials, scaffolds were manufactured varying iteratively one parameter while maintaining constant the other ones. The morphology of the structures was investigated using a scanning electron microscope (SEM), whilst the mechanical performance was assessed though compression tests. Findings – Experimental results highlight a direct influence of the process parameters on the PCL scaffolds properties. In particular, DV and SRV have the highest influence in terms of road width (RW) and consequently on the porosity and mechanical behaviour of the structures. Research limitations/implications – The effect of process and design parameters on the biological response of scaffolds is currently under investigation. Originality/value – The output of this work provides a major insight into the effect of process parameters on the morphological/mechanical properties of PCL scaffolds. Moreover, the potential and feasibility of this novel extrusion-based system open a new opportunity to study how structural features may influence the characteristics and performances of the scaffolds, enabling the development of integrated biomechanical models that can be used in CAD systems to manufacture customized structures for tissue regeneration.