Greetings.
Initial database should have a main index listing of employees. This could have a unique employee number (if it exists) or last name, first name. A larger group may require this to be categorized under various departments.
Physical files should have an approach in dividing it into two sections: employee data & correspondence. The first section should be built on standard forms compiled by HR, which should cover Employee information, emergency contact, medical history (blood group/allergies/medication), next of kin, etc. The second section would consist of all related correspondence filed date-wise.
Again, this could be simple or get complex depending on the nature & size of the organization. If the company also adopts to have them in electronic form, you would need to adopt issuing soft copy formats for getting employee info & relevant correspondence would need to be scanned and filed electronically. Ideally, a single file should be kept for each person.