Hi Riddhiman,
If you are an employee of a MNC co. and i/c of Payroll first pl.check, I am sure they will have HR policies and Payroll software/package, if yes you should study them as they will prefer to adopt the same here. If you wish to know the details for knowledge sake then you note these -
You should study the HR policy, especially, no.of employees, salary structure individually, components of salary, nature of deductions. Also you should conduct a system study' into order to finalise as what should be the hardwares, OS, platform, and programme/language, and have them documented properly with the help of SW consultants.
Once the above are finalised you have to organise time office, linking its systems and attendance records. Have a test run and check all parameters are working fine for accuracy. These are to be handled by professionals and experienced persons.