Cell free layer (CFL), a plasma layer bounded by the red blood cell (RBC) core and the endothelium, plays an important physiological role. Its width affects the effective blood viscosity as well as the scavenging and production of nitric oxide (NO). Measurements of the CFL and its spatio-temporal variability are highly uncertain, exhibiting random fluctuations. Yet traditional models of blood flow and NO scavenging treat the CFL's bounding surfaces as deterministic and smooth. We investigate the effects of the endothelium roughness and uncertain (random) spatial variability on blood flow and estimates of effective blood viscosity.