A system and method for selective masking of stents using an expandable masking balloon to prevent deposition of therapeutic or protective coatings on portions of the stent during a coating application process. An expandable balloon is located within the inner region of a stent, the balloon is inflated until its outer surface contacts and the inner surface of the stent lattice in the areas in which the stent coating is not to be applied, thereby masking the stent inner surface from deposition of stent coating material during a stent coating process, and the coating is applied to the remaining exposed surfaces of the stent, for example by spraying or dipping the stent. The balloon is then deflated and removed from the coated stent. The balloon may be coated with, or formed from, a material impregnated with polytetrafluoroethylene to discourage adherence of the coating material to the balloon's outer surface in order to minimize coating waste and bridging of stent lattice openings by coating films.

 
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