In a system for stabilizing a pattern of structural changes in corneal fibrils, an eye treatment system causes corneal fibrils of a cornea of an eye to transition from a first structure to a second structure. An application device applies a cross-linking element to the corneal fibrils. An activating device applies an initiating element to the corneal fibrils and activates the cross-linking element. The cross-linking element causes cross-linking in the corneal fibrils to preserve the second structure of the corneal fibrils. Another application device may apply a cross-linking breaker to the corneal fibrils. The cross-linking breaker halts or reverses at least partially the cross-linking in the corneal fibrils. Another activating device applies an initiating element to the corneal fibrils and activates the cross-linking breaker. Advantageously, the cross-linking breaker provides greater control over the amount and progress of cross-linking that occurs in the corneal fibrils.