The bonus point 29-0 final group game win on the road in west Wales against the Scarlets was good enough to earn them the second best ranking position and that all-French showdown against Montpellier.
It means France are guaranteed at least one team in the semi-finals with Cotter adding: "We are wrapped to get a home quarter-final, especially given we were in a Pool with Leinster.
"A home quarter-final is crucial in this tournament and especially to have a game in Clermont where we have a proud record.
"We're very happy for our supporters because it's the first time they will have a crack at a quarter-final and their enthusiasm will bring our team along for what will be a tough game."
Clermont made it six from six but had to concede the top ranking spot to Harlequins on overall try count.
"We did what we said we were going to do which is pleasing from a coaching view and we never gave up a try in the second half which shows we can keep our discipline and show character," said Cotter.
"We will need those qualities if we are going to progress in this competition.
"Our game was heavily built upon the first 20 minutes. We knew Scarlets are a team we had to get to grips with, especially in the physical contact because they are a good side that can threaten, as they showed in the second half.
But we managed to stop them early on and that created a couple of lucky breaks and we took the chances as well as score a couple of nice tries.
The second half was more about them attacking and us defending but we handled that well enough which was very encouraging for all coaches.