MacLean told reporters after Tuesday's skate that the surgery was to clean up debris in the knee.
The injury caused Michalek to miss 10 games earlier this season. He came back for two games in early March, picking up an assist in each game, but found the knee continued to bother him.
Michalek has two points and eight assists in 15 games with the Senators this season. He had a breakout season in 2011-12, with 35 goals and 25 assists in 77 games.
The Senators' lineup has been hit hard this year, with star centre Jason Spezza, Norris Trophy-winning defenceman Erik Karlsson and starting goaltender Craig Anderson all out with long-term injuries.