Does methotrexate affect the. Eyes? If yes how can it be prevenred from. Harming the eye?

No. Methotrexate does not harm the eyes in any way. In fact, low dose weekly Methotrexate is an excellent treatment for autoimmune inflammation of the eyes (called uveitis). It is actually much safer than long term steroids (eye drops or oral) since long term use of steroids can cause cataracts and other eye problems.
No. Methotrexate does not affect the eyes but several of the diseases that Methotrexate is used to treat can have eye issues.