Three-dimensional (3D) bioplotting is a melt-extrusion-based additive manufacturing process used to fabricate 3D scaffolds for tissue engineering applications. This study investigates the relationship between material rheology, process parameters, and scaffold characteristics during 3D bioplotting of polycaprolactone (PCL). The effects of two process parameters, extrusion temperature and nozzle diameter, on resultant scaffold structure and compression strength were studied using design of experiments. PCL scaffolds designed for a 24-well culture plate (Ø 14 mm × 2 mm) were bioplotted in a 0°/90° laydown pattern at three levels of extrusion temperature (80°C, 90°C, and 100°C) and two levels of nozzle inner diameter (0.3 and 0.4 mm) at a constant extrusion pressure (0.35 N/mm2) and nozzle speed (1.2 mm/s). The relationship between PCL dynamic viscosity and extrusion temperature during bioplotting was then determined using rheological measurements. The ANOVA results demonstrated that the strand width and porosity significantly varied as a function of the extrusion temperature, the nozzle inner diameter, and the interaction of the two parameters (p < 0.05). The compression modulus of scaffolds fabricated at the different experimental levels also showed an increasing trend (0.5 – 0.97 MPa) with extrusion temperature for a given nozzle diameter. Rheological analysis at the three extrusion temperatures showed the average viscosity to be significantly different at each level (p < 0.05). The apparent viscosity of PCL at the nozzle tip during 3D bioplotting was also estimated, showing a steep decrease with increasing extrusion temperature and nozzle diameter. Finally, predictive regression models to estimate the scaffold characteristics based on the 3D bioplotting process parameters were developed.