Letting Copper sit in NaOH for 5 min (for monolayer assembly)
Such steps are usually cleaning steps to remove deposited organic materials. $\ce{NaOH}$ is also known as lye and will dissolve basically all organics. In this case, it should leave the $\ce{Cu}$ and copper oxides alone, leaving a clean surface.

I don't have as much experience with copper monolayers, but similar cleaning steps are used in my lab, where you might treat with ozone or some other step to remove any deposited organic "gunk" from the metal surface.

In this case, I believe you don't want to use an acid, because the thiols react with the copper oxide surface, not strictly the copper itself.