Trapping macromolecules in nanopits finds diverse applications in polymer separation, filtering biomolecules etc. However, tuning the locomotion of polymers in channels of nanoscopic dimensions is greatly restricted by the comparative advective and diffusive components of velocities. Using the polymer affinity toward the solvent and the wall, and the polymer structure, a mechanism is proposed to induce selective trapping of polymers. Similar to fractional distillation of hydrocarbons based on molecular weight, a technique of fractional segregation, depending on the channel wettability of polymeric chains at different depths in a pit that is located perpendicular to the flow is suggested. Depending on the properties of the polymeric chains and the surface chemistry, the segregation of the polymer at a particular level in the pit can be predicted. This behavior stems from the difference in polymer structure leading to a competition between wettability based enthalpic trapping and structure based entropic trapping. The results of this study suggest a novel way of separating biopolymers based on their structure without relying on the channel geometry. (C) 2016 Wiley Periodicals, Inc.