The sentence is "Instruct staff assistant to create hard copy folders of employment files" what does the "hard copy folders" here mean? I don't understand "hard" at all. Does it mean the duplicate documents from copier?
Instruct staff assistant to create hard copy folders of employment files
This probably means make a folder to contain hard copies of employment files. A "hard copy" is as @QuokMoon says a printed or physical version of a computer file. The person telling you this is probably assuming you know that they keep a scan or PDF of various documents on a computer, and they want you to make a folder to also to put printouts of these.
Now, it's also possible that "file" can mean "packet or set of all employment documents that need to be kept together". In that case what this person likely means is for you to print out all that information, make a folder for it, and put everything in the folder. Basically make one folder for each person's set of documents.
You should ask the person telling you this for clarification as either thing could be meant.
A "hard copy folder" is a retronym phrase for a paper folder of printed material.
Other examples of retronyms include "cloth diaper" (once diapers were assumed to be cloth), acoustic guitar (before the electric guitar), et cetera. Just as "acoustic guitar" anticipates the fact that a "guitar" may now be electric, a "hard copy folder" anticipates the fact that a "folder" may now be digital.
Once "hard copy folder" would have been redundant. Then the word "folder" was adopted in computing as part of the "desktop metaphor," beginning with work at Xerox PARC in the 1970s. When desktop user interfaces became popularized in the 1980s and 1990s words like "desktop," "trash," "file," and "folder" also came to mean digital data and digital user interfaces, not just objects of wood and paper. These digital forms are all virtual "software." By contrast with the "soft" digital copy, the physical paper copy is described as the "hard copy."
Returning to the example:
"Instruct staff assistant to create hard copy folders of employment files"
This states that the "folders" are paper, and also implies that, by contrast, the "employment files" that are being copied are digital files, not paper files. Once we guess that the employment files are digital we know that "create" means "print out with a printer" and not "duplicate with a copy machine."
"Hard copy" is a phrase used mostly in relation to computers.
A printed version on paper of data held in computer.