While their opponents qualified for the knockout rounds with a 100 percent record, Chelsea progressed despite just winning one of their three home games, giving Bayern further cause for optimism ahead of Tuesday's fixture in the English capital.
However, Flick has been impressed by the Blues this season, believing they are punching above their weight in the Premier League under Frank Lampard.
"My team knows what to expect and we want to be brave, confident and attack," Bayern's head coach told the media. "I'm really full of confidence we can put in a good performance.
"We've analysed their strengths and weaknesses, the chances we see where we can decide the game for us.
"I think they play very well, and they have built a new team. They're very good, fourth in the Premier League and several teams are behind them that you thought would have been ahead of them.
"We're going to show respect, but we will not be full of fear."
On opposite number Lampard, Flick added: "He's doing a really good job. He's been successful in the Premier League by getting to fourth. They look like they will qualify for the Champions League. A great job.
Flick – who celebrated his 55th birthday on Monday – confirmed Leon Goretzka should be available after training with the squad prior to their flight from Germany.
Philippe Coutinho will also hope to feature after starting Friday's 3-2 league win over Paderborn, with the subject of the Brazilian's form once again raised during Bayern's pre-match press conference.
Asked about Coutinho's lack of consistency since joining the club, Flick said: "I'm always positive when I look at how he plays in training. He's football mad.
"Sometimes he is putting himself under too much pressure. He always tries to give his own mark on the game, so every decision he makes is generally right, but we will always support him.
"I think a lot of him as a player and a human being."