How can we remove an employee from our visa and labor system?

Good Day,

We are an education sector company.

How can we remove an employee from our visa/labor system if he/she has already exited the country without proper signing of the official cancellation papers?

They provided us with resignation after exiting the country. The employee even though resigned, occupies a dead space on our quota and this is very frustrating when we want to add or replace with another employee.