Plzen's 5-0 aggregate thrashing of Napoli in the last round, coupled with their domestic form which has taken them to the top of the Czech League, makes them big favourites against the Turkish side.
But ahead of Thursday's first leg at the Doosan Arena in Plzen, Kolar warned it will not be a straightforward task for his team.
"People are saying it will be easier than Napoli, but Fenerbahce are a top European team with some great players," he said.
Plzen, whose domestic draw with Banik Ostrava at the weekend ended a run of five straight wins, are boosted by the return of captain Pavel Horvath, who missed the Banik game due to illness.
Meanwhile, Fenerbahce travel to the Czech Republic on the back of two straight losses against Trabzonspor in the Turkish Cup and then Besiktas in the Super Lig, a defeat which saw them drop to third.
Coach Aykut Kocaman's problems are also heightened by the losses of both Egemen Korkmaz and Raul Meireles through suspension, while Emre Belozoglu also misses out.
Kocaman knows his side face a big test, saying: "Plzen are a very good team with very good physical strength. But getting through the group stages has really boosted our confidence."