Polycaprolactone (PCL) is a biodegradable thermoplastic polyester with widespread use in biomedical applications. Recently it has been used in 3D bioplotting to produce scaffolds and other biomedical devices. However, the effect of material properties, such as rheological and thermal properties on this microextrusion process have not been investigated. In this work we first use PCL having different molecular weights to produce miscible blends of varying viscosities and we investigate the effect of processing parameters, including needle length and diameter and dispensing pressure on the extrusion shear rates, shear stresses, pressure drops and the swell ratio of the extruded strands. We further identify relevant dimensionless numbers that reflect the material rheological properties and processing conditions. Based on these results we define ranges of operation in 3D bioplotting. Furthermore, we modify PCL using an elastomeric poly(3-hydroxyoctanoate) P(3HO). Even though addition of the amorphous P(3HO) results in a decrease in the crystallinity of PCL, the crystallization temperature of the blends increases, and the blends exhibit faster crystallization rates. Compositions ranging from 10-30 wt% P(3HO) are ideal for processing, because of their improved crystallization kinetics, reduced stickiness and good flow properties. The extruded blend fibers exhibit fine morphology, resulting in synergistic effects in thermal and mechanical properties.