The dynamic interaction between cells and their substrate is a cornerstone of biomaterial-based tissue regeneration focused on unraveling the complex factors that govern this crucial relationship. A key challenge is translating physical cues from 2D to 3D due to limitations in current biofabrication techniques. In response, this study introduces an innovative approach that combines additive and subtractive manufacturing for precise surface patterning of 3D printed scaffolds. Using poly(𝜀-caprolactone) as the scaffold material, polymeric fibers are 3D printed and subsequently laser-engraved with femtosecond laser to precisely create controlled microtopographies, including microgrooves (10 and 80 µm in width) and micropits (25 µm in diameter). Testing shows that the process does not compromise the mechanical properties of the fibers, which is critical for structural applications in tissue engineering. Human mesenchymal stem cells are used to investigate the effects of these topographical features on cell behavior. The 10 µm wide microgrooves notably enhance cell attachment, with cells aligning in elongated forms along the grooves, while micropits and unpatterned surfaces promote polygonal cell shapes. This combined approach demonstrates that precisely engineered microtopographies on 3D printed scaffolds can better mimic the natural extracellular matrix, improving cellular responses and offering a promising strategy for advancing tissue regeneration.