The US space agency had identified two "gap fillers" that were sticking out between heatshield tiles near Discovery's nose section, each by less than 3cm (1.2in).
Experts said protrusions on the otherwise smooth belly of the shuttle could disturb the air flow during re-entry, causing turbulence that raises temperatures on heatshield tiles downstream.
Discovery will take parts and supplies to the ISS and test new safety features such as a repair-kit for heatshield tiles and a 15m-long robotic arm that will inspect the shuttle for damage in orbit.