Both past perfect and past perfect continuous tenses indicate an action that began and was completed in the past. The difference is that past perfect continuous also implies an element of duration. "It had been raining" and "It had rained" mean almost the same thing, except for a difference in emphasis: "It had been raining" = emphasis on the duration of time, it was a continuous (but ultimately finished) action "It had rained" = the rain was a single event, not a process over time