Generally, when a non-Singapore Citizen employee (i.e. foreign or Singapore Permanent Resident employee) ceases employment with the company in Singapore, goes on an overseas posting or plans to leave Singapore for more than three months, the employer is required to seek tax clearance for him/her.
As an employer, you have the responsibility to file the Form IR21 and withhold all monies due to the employee for tax clearance purpose. This applies to all work pass holders including Personalised Employment Pass (PEP) holders.
If you would like to withhold their salaries for tax, do create a "Deduction (from Net Salary)(No SHG contribution)" pay item in Ad Hoc Payment / Deduction tab under Payroll > Payroll Settings > Process Payment - Step 2. Leave the remarks as "Tax withhold for IR21 clearance".