The Gunners host the npower Championship side just four days ahead of their showdown with the Bundesliga giants at Emirates Stadium. It is the start of a crucial period which could well define Arsenal's season, as they go to Tottenham on March 9 and then host Everton before travelling to the Allianz Arena for the second leg.
German centre-back Mertesacker said as part of adidas 'football Hangout on air' webchat: "We still have an important cup game on Saturday (first) - we absolutely want to advance in the FA Cup, that is why the preparations for Bayern are not that intense yet."
He added: "However, beginning on Sunday the preparations for Tuesday's match will be extreme. Bayern are doing superb this year and that is a big challenge for us, but we are looking forward to both legs."
The Germans have not lost since October 28 and have opened up a massive 15-point lead at the top of the Bundesliga, maintaining their ominous form with four straight wins following the winter break.
Former Arsenal and Germany goalkeeper Jens Lehmann believes his old club will face a real challenge to progress further in the competition against last season's beaten Champions League finalists.
Writing in a column for the Sport Bild magazine, Lehmann said: "For an English team it is the worst draw to play a German team directly after the winter break.
"In addition to that Bayern has not been really challenged for once yet in the second half of their season. The only stress they have is the one at the training sessions."
However, Lehmann, 43, believes Arsenal have the players to cause Bayern problems.
He added: "(Bayern coach) Jupp Heynckes will warn his players of the speed that Arsenal still can play in the offensive game, especially Theo Walcott but also more and more Lukas Podolski can be very dangerous. Vice-versa, Arsenal will look to stop Bayern creating their good positioning game from which they can accelerate."