Benzema joined Real Madrid from Lyon in 2009 and Modric arrived from Tottenham in 2012, the pair winning five Champions Leagues with Real Madrid among other trophies.
Kroos joined Madrid from Bayern Munich in 2014, winning the Champions League on four occasions with Los Blancos.
Asked about Kroos and Modric, Ancelotti said he believed a "solution" would be found.
"There are advances, because they are talking," said Ancelotti.
"I think that in the end they will look for a solution, there are advances."
The coach also thought Benzema, who scored a hat-trick in the emphatic 4-0 win over Barcelona on Wednesday in the Copa del Rey semi-final, would stay.
However, the Italian warned that at some point, Madrid would have to move on.
"I think (the three) will stay," said Ancelotti. "But we have to think about the day they stop too, because, for the fact they have something unique, something will have to change.
"We have to look for the club's future along a different line, not the way (we play) with Kroos and Modric.
"We have fantastic young players, (Eduardo) Camavinga, (Aurelien) Tchouameni, (Fede) Valverde and (Dani) Ceballos, who will mark an era at Madrid, but in a different way to Kroos, Modric and Casemiro."
Ancelotti still believes that Benzema, Modric and Kroos are offering Madrid a lot, even if physically they are past their peak.
"We have to evaluate the players not by their age but by what they do," added the coach.
"You can think the three don't have the physical profile or energy of the younger players, but what these three have in terms of game management is unique, you can't buy it on any market in the world.
"This is born with experience -- age takes something from you, but it gives you something back as well."