Recent advances in regenerative medicine have improved understanding of the materials properties of nanofibrillar scaffolds used to aid cell system re-establishment. A picture is emerging that a successful scaffold has a defined set of physical properties including mechanical properties, topographical properties, and growth factor inclusion, and that the weighting of each may vary depending on the cell system and its functionality. In the present work, results from investigations of a slowly biodegradable nanofiber prosthetic for neural cell system re-establishment are presented. Preliminary data from in-vivo investigations (rat model) indicate that a nanofiber prosthetic device of FGF-2-modified nanofibers contributes to system re-establishment including aligned guidance for regenerating axons across an injury gap, and angiogenesis. Research by Meiners’ group also demonstrated that FGF-2 retains biological activity significantly longer when immobilized on nanofibers than when presented as a soluble molecule [1]. The present investigations use atomic force microscopy operated in a new mode, Scanning Probe Recognition Microscopy (SPRM) [2], developed by Ayres’ group, to quantitatively investigate properties of FGF-2-modified nanofibers. The SPRM system is given the ability to auto-track on regions of interest through incorporation of recognition-based tip control realized using algorithms and techniques from computer vision, pattern recognition and signal processing fields. Statistically meaningful numbers of reliable data points are extracted using an automatic procedure that maintains uniformity of experimental conditions. Properties under quantitative SPRM investigation include nanofiber stiffness and surface roughness, nanofiber curvature, nanofiber mesh density and porosity, and growth factor presentation and distribution. Each of these factors has been demonstrated to have global effects on cell morphology, function, proliferation, morphogenesis, migration, and differentiation.[1] A. Nur-E-Kamal et al., Mol Cell Biochem 309 (2008) 157-166.[2] Y. Fan et al., Int. J. Nanomedicine 2 (2007) 651-661.