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Abstract Conventional dialyzer membranes typically comprise of unevenly distributed polydisperse, tortuous, rough pores, embedded in relatively thick ≈20–50 µm polymer layers wherein separation occurs via size exclusion as well as differences in diffusivity of the permeating species. However, transport in such polymeric pores is increasingly hindered as the molecule size approaches the pore dimension, resulting in significant retention of undesirable middle molecules (≥15–60 kDa) and uremic toxins. Enhanced removal of middle molecules is usually accompanied by high albumin loss (≈66 kDa) causing hypoalbuminemia. Here, the scalable bottom‐up fabrication of wafer‐scale carbon nanotube (CNT) membranes with highly aligned, low‐friction, straight‐channels/capillaries and narrow pore‐diameter distributions (≈0.5–4.5 nm) is demonstrated, to overcome persistent challenges in hemofiltration/hemodialysis. Using fluorescein isothiocyanate (FITC)‐Ficoll 70 and albumin in phosphate buffered saline (PBS) as well as in bovine blood plasma, it is shown that CNT membranes can allow for significantly higher hydraulic permeability (more than an order of magnitude when normalized to pore area) than commercial high‐flux hemofiltration/hemodialysis membranes (HF 400), as well as greatly enhance removal of middle molecules while maintaining comparable albumin retention. These findings are rationalized via an N‐pore transport model that highlights the critical role of molecular flexing and deformation during size‐selective transport within nanoscale confinements of the CNTs. The unique transport characteristics of CNTs coupled with size‐exclusion and wafer‐scale fabrication offer transformative advances for hemofiltration, and the obtained insight into molecular transport can aid advancements in several other bio‐systems/applications beyond hemofiltration/hemodialysis.