Sub-epithelial infiltrates resulting from EKC can persist for years. They are collections of inflammatory cells under the surface of the cornea. They do gradually resolve; when they cause significant symptoms, your ophthalmologist could put you on a topical steroid, which will accelerate the clearing of the infiltrates. You need to be followed closely by the ophthalmologist, because long-term steroids can cause cataracts and glaucoma. There are milder steroids such as Alrex or Lotemax which could be tried.