Cell-based therapies and tissue engineering applications require biocompatible substrates that support and regulate the growth, survival, and differentiation of specific cell types. Extensive research efforts in regenerative medicine are devoted to the development of tunable biomaterials which support various cell types including stem cells. In this research, the non-cytotoxic biopolymer polycaprolactone (PCL) was fabricated into 2D and 3D scaffolds with or without the low-pressure oxygen plasma treatment to enhance hydrophilicity. Cellular responses and biocompatibility were evaluated using a human Wharton’s jelly mesenchymal stem cell line (BCP-K1). The 2D PCL scaffolds enhanced initial cell attachment compared to the 3Ds indicated by a higher expression of focal adhesion kinase (FAK). Whilst, the 3D scaffolds promoted cell proliferation and migration as evidenced by higher cyclin A expression and filopodial protrusion, respectively. The 3D scaffolds potentially protected the cell entering to apoptosis/necrosis program and induced cell differentiation, evaluated by gene expression. Both 2D and 3D PCL appeared to have stronger effects on cell behavior than a control substrate (polystyrene). In summarize, the different configuration and surface properties of PCL scaffolds provide various options for modulation of stem cell behaviors, including attachment, proliferation, survival, and differentiation, when combined with specific growth factors and culture conditions.