The Bavarian giants thrashed Shakhtar Donetsk 7-0 on Wednesday to reach the UEFA Champions League quarter-finals in stunning fashion.
Shakhtar's Olexandr Kucher was shown the quickest red card in the history of Europe's premier club competition and his third-minute dismissal paved the way for Bayern's win, which saw six different players score.
And it was bad news for a Werder side who have conceded at least five goals in all of their last four matches against Bayern.
Pep Guardiola's men have won their last nine meetings against Werder in all competitions, but have stepped the victories up a notch since a 6-1 home triumph in February 2013.
A 7-0 away win followed in the December of that year and Bayern have backed it up with 5-2 and 6-0 successes in front of their home fans.
"We're very hot [at the moment]," Muller told UEFA's official website. "We're looking forward to the future."
Bayern's win was somewhat soured by Arjen Robben's withdrawal with a trapped nerve after 19 minutes, while Franck Ribery sustained a sprained ankle during the second half.
"We have a great squad but of course every single injury hurts us," he added. "We were hoping that nothing major would happen but, as far as I know, things are not dramatic."
Although a third consecutive Bundesliga crown was always likely, Wolfsburg's defeat at Augsburg last week handed Guardiola's men a major boost.
Werder were also victorious on the road, as Franco Di Santo's stunning strike handing them a 1-0 success at Freiburg.
The ex-Chelsea and Wigan Athletic forward has been a key figure in Werder's resurgence, which has seen them win six of their last eight Bundesliga matches.
Philipp Lahm returned to Bayern's matchday squad on Wednesday following more than three months on the sidelines with an ankle injury and could play a part for the visitors.
