Linux user permissions. If you own/run your own web server, you can chown certain directories you don't want certain users to have access to etc. Whatever FTP server you're using will then adhere to these permissions (WASlayer assumes you're using FileZilla Server since you mention the FileZilla client as well, which is rarely the case in the real-world)
You can do this via CPanel if you're using that to administer your web server.
But to give you step-by-step advice and/or what you need to achieve this, we would need to know:
1) Server OS
2) Cpanel/WHM Installed?
3) FTP Server software (if not Filezilla on server AND client)
4) How much you're willing to pay for a tailor-made step-by-step guide for your specific situation