A 33-year-old male presented with unilateral subacute infectious keratitis 4 weeks after surgery. Corneal inflammation was resistant to standard topical antibiotic regimens. During diagnostic flap lifting and sampling, the corneal flap melted and separated. Through flap lifting, corneal scraping, microbiological diagnosis of atypical mycobacteria, and treatment with topical fortified amikacin, clarithromycin, and systemic clarithromycin, clinical improvement was achieved.