With a huge changing of the guard to come for the Cardiff outfit this summer the clash with Leinster was the end of an era for the likes of Gethin Jenkins, Casey Laulala and Martyn Williams.
With Rhys Thomas, Richie Rees and Dan Parks also departing in the summer the Blues look set to enter into a tough-looking transitional period.
And Baber is the first to accept some tough times await for his side.
"We're going through a bit of pain at the moment," said Baber.
"And probably we'll go through a little bit more pain in the next year but we have to develop a new crew of players.
"That is why we're recruiting the players we have and developing our own - and that has to be the focus of the next couple of years at the Cardiff Blues."
But Baber insists all is not lost in this campaign.
"We want to finish as high as we can in the Pro 12," he added. "It is tough, it is a tough stage of the season and everybody is tired," said Baber.
"We're all hurting as it is not nice to be where we are at. We have to make sure we come out with something positive before the end of the season."
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