The best way to identify a snake hole is to actually see a serpent gliding in or out. If you haven't, use a stick to check for vacancy or install a camera while exercising caution.
Your goal now is to get rid of the holes by filling and covering them. Start by smashing dirt firmly into the opening, or combine compacted soil and stones to plug the space.
Another option is to stuff steel wool into the pit as its density inhibits a snake's ability to move — moreover, the limbless reptile is unable to chew through it.