Fundamental insight into the extent to which the nanostructured surface and geometry impacts neurochemical interactions at electrode surfaces could provide significant advances in our ability to design and fabricate ultrasensitive neurochemical detection probes. Here, we investigate the extent to which the nanostructure of the carbon-fiber surface impacts detection of catecholamines and purines with fast-scan cyclic voltammetry (FSCV). Carbon-fibers were treated with argon (Ar) plasma to induce variations in the nano- and micro-structure without changing the functionalization of the surface. We tested variations in topology by measuring the extent to which the flow rate, RF power, and treatment time affect the surface roughness. Flow rates from 50-100 sccm, plasma power from 20-100 W, and treatment times from 30 s to 5 min were compared. Two Ar-treatments were chosen from the optimization studies for comparison, and the surface roughness was evaluated using atomic force microscopy (AFM). To ensure no changes in chemical composition, fibers were analyzed with X-ray photoelectron spectroscopy (XPS). On average, at the optimized Ar-plasma treatment procedure, oxidative current for adenosine and ATP increased by 3.5 ± 1.4-fold and 3.2 ± 0.6-fold, and guanosine and GTP by 1.7 ± 0.3-fold and 1.8 ± 0.3-fold, respectively (n = 9). Dopamine increased by 1.7 ± 0.3-fold. The extent to which changes in the electrode structure impact adsorption, sensitivity, and electron transfer rates were measured. A COMSOL Multiphysics simulation was developed to enable the modeling of mass transport of electroactive species at varying electrode geometries. Overall, this study provides critical insight into the extent to which the nanostructure of the surface impacts the electrochemical detection of neurochemicals.