The past perfect subjunctive is what you had done, that conveyed a wish, mood, doubt etcetera.

The boss doubted that she had filed the letters.  (imperfect, past perfect subjuntive)

To form take imperfect subjunctive of haber + past participle

La jefa dudaba que el secretario hubiera archivado las cartas.

Me alegré que hubieras salido bien en la entrevista.

I was(preterite) happy that you had done well in the interview.

Para el puesto, sería que ustedes hubieran estudiado español.

For the postion, it would be better that you had studied Spanish.

Era importante que me hubieras dicho la verdad.

It was important that you had told me the truth.

Angelica se alegró de que su novio le hubiera escrito la semana pasada.

Angelica was happy that her boyfriend had written her last week.