Thanks for your answer. Can we use both of them in following sentence?
"This form should be filled out by/with the applicant."
You could use either of them, depending on what meaning you want to convey.
If this is an instruction for the applicant and you want them to fill it out by themselves, then say "by."
If this is an instruction to some sort of "helper" and this "helper" will help the applicant fill out the form, then say "with."