In all the cleanrooms I have been in face masks have been required. Human breath has a lot of water droplets in it.
How are you going to get a face recognition off someone in clothes like this?
The employees are not allowed to take off their face mask for a scan. Suggesting it would get you laughed at and fired at the places where I worked.
Just use RFID scanners with the access badges they already have or with RFID bracelets like mentioned in other posts. For additional security: have a guard at the door. Once an employee checks in have him verify that it's the right person with a picture on his screen.
Or facial recognition there. Before the face mask goes on.