The Germany duo took part in a full session on Monday, with Neuer expected to start in goal against the European champions after recovering from foot surgery that forced him to miss Bayern's last three games.
Mueller has shaken off an ankle injury that saw him sit out the past two matches and also hopes to feature at the Allianz Arena.
"I could take part in normal training, which is a good sign," said Mueller. "We are well prepared and full of confidence.
"This is a huge European match between two top teams. Of course the anticipation is huge."
Bayern's top scorer Robert Lewandowski, who has scored seven Champions League goals this season in a haul of 38 in all competitions, trained alone after injuring his shoulder against Borussia Dortmund but is fit to play.
However, defender Mats Hummels is sidelined after tearing a ligament in his right ankle in training on Sunday and faces a race to be fit for the return leg in Madrid on April 18.
"I definitely won't be on the pitch on Wednesday," told German daily Bild.
"Very sad about missing at least the next two games," the centre-back added on Twitter while posting a picture of himself wearing a special recovery boot on Instagram under the caption, "Already trying to recover as fast as possible".
As well as this week's Champions League first leg, Hummels will sit out Saturday's Bundesliga match at Bayer Leverkusen at the very least.
Madrid will be without Pepe after the Portugal centre-back broke two ribs in the 1-1 draw with Atletico Madrid on Saturday and French defender Raphael Varane will also miss Wednesday's game.