Introduction The use of scaffolds in tissue engineering is becoming increasingly important as solutions need to be found for the problem of preserving human tissue, such as bone or cartilage. In this work, scaffolds were printed from the biomaterial known as polycaprolactone (PCL) on a 3D Bioplotter. Both the external and internal geometry were varied to investigate their influence on mechanical stability and biocompatibility. Materials and Methods: An Envisiontec 3D Bioplotter was used to fabricate the scaffolds. First, square scaffolds were printed with variations in the strand width and strand spacing. Then, the filling structure was varied: either lines, waves, and honeycombs were used. This was followed by variation in the outer shape, produced as either a square, hexagon, octagon, or circle. Finally, the internal and external geometry was varied. To improve interaction with the cells, the printed PCL scaffolds were coated with type-I collagen. MG-63 cells were then cultured on the scaffolds and various tests were performed to investigate the biocompatibility of the scaffolds. Results: With increasing strand thickness and strand spacing, the compressive strengths decreased from 86.18 + 2.34 MPa (200 µm) to 46.38 + 0.52 MPa (600 µm). The circle was the outer shape with the highest compressive strength of 76.07 + 1.49 MPa, compared to the octagon, which had the lowest value of 52.96 ± 0.98 MPa. Varying the external shape (toward roundness) geometry, as well as the filling configuration, resulted in the highest values of compressive strength for the round specimens with honeycomb filling, which had a value of 91.4 + 1.4 MPa. In the biocompatibility tests, the round specimens with honeycomb filling also showed the highest cell count per mm², with 1591 ± 239 live cells/mm2 after 10 days and the highest value in cell proliferation, but with minimal cytotoxic effects (9.19 ± 2.47% after 3 days).