I want to know if we can use "yet" in the past perfect as we use it in present perfect.
Has he finished yet?
* Had he finished yet?
In this usage of 'yet' meaning 'up to the present time' then I don't believe you can.
"Yet" means "up to the present" when used in the present perfect.
'Yet' means "up to the time in the more recent past that has been referred to" when used in the past perfect.
"Mike was held up at the start of the motorbike race, because he hadn't started his engine yet." 'Yet' refers to the time the race started.
"Peter proposed to Jenny, but he hadn't bought a ring yet." 'Yet' refers to the time at which he proposed.