Hi!
As Lori said, handling by hand is totally fine, the eggs are pretty sturdy because of their gel coating. The hardest part is gently scraping them off the aquarium plant and rocks without squeezing the eggs. You can use a finger nail, or a blade and just scrape across the surface. Whenever possible just allow the eggs to hatch while still attached. (They don't take long to hatch, maybe 2 weeks tops depending on water temp).
And another note on the other piece Lori added. I made the same mistake and kept too many babies. I kept about 150 eggs, and about 145 hatched healthy! This did allow me to make selections of the ones that hatched. It was a hard decision, but of the ones I wasn't able to give away I chose only the healthiest to rear and the rest were culled early on.
Hope that helps