Building 3D electrospun macrostructures and monitoring the biological activities inside them are challenging. In this study, 3D fibrous polycaprolactone (PCL) macrostructures were successfully fabricated using in-house 3D electrospinning. The main factors supporting the 3D self-assembled nanofiber fabrication are the HPO additives, flow rate, and initial distance. The effects of solution concentration, solvent, HPO concentration, flow rate, initial distance, voltage, and nozzle speed on the 3D macrostructures were examined. The optimal conditions of 4 mL/h flow rate, 4 cm initial nozzle-collector distance, 14 kV voltage, and 1 mm/s nozzle speed provided a rapid buildup of cylinder macrostructures with 6 cm of diameter, reaching a final height of 16.18 ± 2.58 mm and a wall thickness of 3.98 ± 1.01 mm on one perimeter with uniform diameter across different sections (1.40 ± 1.10 μm average). Oxygen plasma treatment with 30-50 W for 5 min significantly improved the hydrophilicity of the PCL macrostructures, proving a suitable scaffold for in vitro cell cultures. Additionally, 3D images obtained by synchrotron radiation X-ray tomographic microscopy (SRXTM) presented cell penetration and cell growth within the scaffolds. This breakthrough in 3D electrospinning surpasses current scaffold fabrication limitations, opening new possibilities in various fields.