Concerns over utilizing autogenous cancellous bone grafts (such as donor-site morbidity, increased surgical time/complication rate, and restricted availability) as the gold-standard treatment for critical-sized defects in bone have motivated the development of a wide variety of sophisticated synthetic bone scaffolds in recent years. In this work, a novel solvent-free template synthesis technique was utilized to fabricate poly(epsilon-caprolactone) (PCL) nanowire surfaces as a building block for the development of three-dimensional bone scaffolds. Bone marrow-derived mesenchymal stem cells (MSCs) were used to characterize the short- and long-term in vitro biocompatibility and cellular response to these surfaces. A 4-week study in rats was conducted to assess in vivo biocompatibility as well. Short-term in vitro studies revealed that PCL nanowire surfaces enhanced MSC response in terms of survivability, viability, cytoskeleton changes, and morphology as compared with control surfaces (smooth PCL and polystyrene). In long-term in vitro studies, nanowire surfaces induced a rapid production of bone extracellular matrix by differentiated MSCs as indicated by accelerated calcium phosphate mineralization, and osteocalcin and osteopontin production. In vivo studies and histological analysis confirmed that nanowire surfaces are biocompatible. Preliminary biodegradation studies were conducted and indicated that rate of PCL biodegradation can, to some extent, be controlled through the inclusion of nanowires and ester-degrading enzymes. In addition to demonstrating enhanced short- and long-term MSC response to PCL nanowire surfaces, this work presents a simple technique for solvent-free fabrication and bioactive molecule encapsulation of biocompatible, biodegradable three-dimensional bone scaffold components and warrants further investigation.